Signal encoding and decoding in multiplexed biochemical assays

ABSTRACT

This disclosure provides methods, systems, compositions, and kits for the multiplexed detection of a plurality of analytes in a sample. In some examples, this disclosure provides methods, systems, compositions, and kits wherein multiple analytes may be detected in a single sample volume by acquiring a cumulative measurement or measurements of at least one quantifiable component of a signal. In some cases, additional components of a signal, or additional signals (or components thereof) are also quantified. Each signal or component of a signal may be used to construct a coding scheme which can then be used to determine the presence or absence of any analyte.

CROSS-REFERENCE

This application is a continuation of U.S. patent application Ser. No.15/914,356, filed Mar. 7, 2018, which is a continuation of U.S. patentapplication Ser. No. 14/451,876, filed Aug. 5, 2014, now U.S. Pat. No.10,068,051, which is a continuation of U.S. patent application Ser. No.13/756,760, filed Feb. 1, 2013, now U.S. Pat. No. 8,838,394, whichclaims the benefit of U.S. provisional applications 61/594,480, filedFeb. 3, 2012 and 61/703,093, filed Sep. 19, 2012. The content of theseapplications is incorporated herein by reference in its entirety.

STATEMENT AS TO FEDERALLY SPONSORED RESEARCH

This invention was made with the support of the United States governmentunder Grant No. 1144469 awarded by the National Science Foundation. Thegovernment has certain rights in the invention.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted in ASCII format via EFS-Web and is hereby incorporated byreference in its entirety. Said ASCII copy, created on Aug. 20, 2014, isnamed 38075-716-301-Seqlist.txt and is 9,260 bytes in size.

BACKGROUND

Multiplexed reactions offer significant advantages over traditionaluniplex reactions, including performance of parallel reactions on thesame sample, use of the same chamber to perform multiple reactions, andthe ability to extract rich information from a sample in a fast andefficient manner. However, to achieve these benefits, multiplexed assaysgenerally require complex reporting mechanisms, namely spectrallyresolved fluorescence or chemiluminescence (e.g., PCR, ELISA), spatiallyresolved signals (e.g., microarrays, gel electrophoresis), temporallyresolved signals (e.g., capillary electrophoresis), or combinationsthereof (e.g., Sanger sequencing). There is a need for multiplexedreactions that can be carried out in a single solution.

SUMMARY OF THE INVENTION

This disclosure provides methods, compositions, systems, and kits forthe multiplexed detection of analytes. In some cases, this disclosureprovides assays that are capable of unambiguously detecting the presenceor absence of each of at least 7 analytes, in any combination ofpresence or absence, in a single sample volume without immobilization,separation, mass spectrometry, or melting curve analysis. In someexamples, each of the analytes is encoded as a value of one (or at leastone) component of a signal.

In some examples, an assay provided in this disclosure is capable ofunambiguously detecting the presence or absence of M analytes, in anycombination of presence or absence, where M=log₂ (F+1) and F is themaximum cumulative value of one component of a signal (e.g., anintensity) when all the analytes are present.

In some cases, each analyte is encoded as at least one first value in afirst component of a signal (e.g., at least one intensity or range ofintensities) and at least one second value in a second component of asignal (e.g., at least one wavelength or range of wavelengths). In someexamples, each analyte is encoded as a first value in a first componentof a signal at each of a plurality of second values in a secondcomponent of a signal (e.g., a signal intensity or range of signalintensities at each of a plurality of wavelengths or ranges ofwavelengths).

In some examples, an assay provided herein is capable of unambiguouslydetecting the presence or absence of M analytes, in any combination ofpresence or absence, where M=C*log₂ (F+1), where C is the number of thesecond values used to encode the analytes and F is the maximumcumulative value of the first component of the signal, for any secondvalue, when all of the analytes are present.

In some cases, an assay provided in this disclosure is capable ofunambiguously detecting the presence or absence of M analytes, in anycombination of presence or absence, where M=(P*T)+1, where P is thenumber of codes per tier in a coding scheme and T is the number oftiers. In some cases, the number of tiers T=log₄ (F+1), and F is themaximum cumulative value of a first component of a signal, for anysecond value, when all of the analytes are present.

In some examples, the first value is an intensity or range ofintensities. In some cases, a coding scheme comprises at least threeintensities or ranges of intensities.

In some cases, the second value is a wavelength or range of wavelengths.In some examples, the coding scheme comprises at least five wavelengthsor ranges of wavelengths.

In some examples, the signal is an electromagnetic signal. In somecases, the electromagnetic signal is a fluorescence emission signal. Insome examples, the intensity of the fluorescence emission signal ismeasured at at least four wavelengths or ranges of wavelengths.

In some cases, an assay provided herein is performed with reagents thatare lyophilized prior to use.

In some cases, a detecting step is performed with reagents comprisinghybridization probes. In some examples, the number of the hybridizationprobes is greater than the number of analytes. In some cases, the set ofhybridization probes comprise one or more hybridization probes specificfor different analytes and comprising an identical fluorophore orcombination of fluorophores. In some examples, a sample is contactedwith at least 18 of said hybridization probes. In some examples, adetecting step is performed with reagents comprising at least one pairof primers. In some cases, at least one pair of primers are capable ofamplifying a region complementary to at least three of saidhybridization probes.

In some examples, the signal that is measured is generated during apolymerase chain reaction. In some cases, the polymerase chain reactionis selected from the group consisting of an end-point polymerase chainreaction, a real-time polymerase chain reaction, a digital polymerasechain reaction, and combinations thereof.

In some examples, at least one cumulative measurement is performed on asolution.

In some examples, at least one analyte is encoded by at least oneadditional value (i.e., at least two values together), wherein the atleast one additional value is selected from the group consisting of avalue from at least one additional component of a signal, a value fromat least one component of a different signal, and combinations thereof.For example, the at least one additional value may be selected from thegroup consisting of a fluorescence emission intensity, a fluorescenceemission wavelength, a Förster resonance energy transfer (FRET) emissionintensity, a FRET emission wavelength, an electrochemical signal, achemiluminescence wavelength, a chemiluminescence intensity, afluorescence bleaching rate, a chemiluminescence bleaching rate, andcombinations thereof.

In some cases, a chromatogram is constructed. The chromatogram may beconstructed by plotting all possible combinations of first values andsecond values for positive control samples for each analyte.

In some examples, at least one of the analytes comprises apolynucleotide. In some cases, the polynucleotide is from a sourceselected from the group consisting of an animal, a plant, a bacteria, afungus, a parasite, and a virus. In some examples, the polynucleotide isfrom a source selected from the group consisting of humanimmunodeficiency virus, herpes simplex virus, human papilloma virus,Plasmodium, Mycobacterium, dengue virus, hepatitis virus, and influenzavirus. In some cases, the polynucleotide is selected from the groupconsisting of human immunodeficiency virus polyprotease, humanimmunodeficiency virus p17, human papilloma virus E6, and humanpapilloma virus E7.

In some cases, a sample is selected from the group consisting of aclinical sample, a food sample, an environmental sample, apharmaceutical sample, and a sample from a consumer product.

In some examples, information concerning the presence or absence of ananalyte is transmitted through a computer network.

In some cases, information concerning the presence or absence of ananalyte is provided to a physician. In some examples, a clinicaldecision is made based on such information.

In some examples, at least one step of a method provided herein isperformed using instructions on a computer readable medium. In somecases, the instructions are located on a remote server. In someexamples, the instructions are located on a thermal cycler. In somecases, the instructions are located on a computer in communication witha thermal cycler.

In some cases, at least one of the analytes is a positive controlanalyte.

In some examples, the coding scheme is non-degenerate. In some cases,the coding scheme is designed to be non-degenerate. In some examples,the coding scheme is made non-degenerate by enumerating every legitimateresult that can be obtained from the coding scheme, identifying eachlegitimate result that is degenerate, and eliminating at least onepotential analyte code from the coding scheme to eliminate degeneracy.

In some cases, an assay provided herein is an end-point assay. In someexamples an assay provided in this disclosure is ended at a thresholdnumber of cycles set by the limit of detection of an instrument.

In certain examples, an assay provided herein is a liquid phase assay.

In some cases, an assay provided herein is quantitative.

In some cases, this disclosure provides a method of detecting thepresence or absence of each analyte of a plurality of analytes,comprising: (a) encoding each of said analytes as a first value of asignal, thereby generating a coding scheme, wherein each of saidanalytes is represented in said coding scheme by said first value,wherein said encoding is performed in a manner that eliminatesdegeneracy; (b) providing a sample comprising, or potentiallycomprising, at least one of said analytes; (c) contacting said samplewith analyte-specific reagents that generate said first value, asrepresented in said coding scheme, when each of said analytes ispresent; (d) cumulatively measuring said first values of said signalwithin said sample, thereby providing a cumulative measurement; and (e)determining whether each of said analytes is present or absent based onsaid cumulative measurement and said coding scheme.

In some examples, the method described in the preceding paragraph iscapable of unambiguously detecting the presence or absence of Manalytes, in any combination of presence or absence, where M=log₂ (F+1)and F is the maximum cumulative value of the first values when all ofthe analytes are present. In some cases, the first value is an intensityor range of intensities. In some examples, the first value has a minimumvalue in the coding scheme that is selected from the group consisting ofat least 1, at least 2, at least 4, at least 8, at least 16, at least32, and at least 64. In some cases, the first value is incremented inthe coding scheme by an amount equal to the cumulative maximum of saidpreceding first values plus one. In other cases, the first value isincremented in the coding scheme by an amount greater than thecumulative maximum of the preceding first values plus one.

In some cases, this disclosure provides a method of detecting thepresence or absence of each analyte of a plurality of analytes,comprising: (a) encoding each of said analytes as at least one firstvalue and at least one second value, wherein said first value is a valuefrom a first component of a signal and said second value is a value froma second component of said signal, thereby generating a coding scheme,wherein each of said analytes is represented in said coding scheme bysaid at least one first value and said at least one second value,wherein said encoding is performed in a manner that reduces oreliminates degeneracy; (b) providing a sample comprising, or potentiallycomprising, at least one of said analytes; (c) contacting said samplewith analyte-specific reagents that generate said at least one firstvalue and at least one said second value, as represented in said codingscheme, when each of said analytes is present; (d) cumulativelymeasuring said first values and said second values within said sample,thereby providing a cumulative measurement; and (e) determining whethereach of said analytes is present or absent based on said cumulativemeasurement and said coding scheme, wherein, when degeneracy iseliminated, said method is capable of unambiguously detecting thepresence or absence of each of at least six analytes in a single volume,in any combination of presence or absence, when each of said reagentsgenerates only one second value.

In some cases, each of the analytes of the method described in thepreceding paragraph is encoded as a first value in a first component ofthe signal at each of a plurality of second values in a second componentof the signal. In some cases, when degeneracy is eliminated, this methodis capable of unambiguously detecting the presence or absence of each ofat least seven analytes in a single volume using four second values. Insome examples, when degeneracy is eliminated, the coding schemecomprises T non-degenerate tiers, wherein T=log₄ (F+1) and F is themaximum cumulative value of the first component of the signal, for anysecond value, when all of the analytes are present. In some cases, whendegeneracy is eliminated, the method is capable of unambiguouslydetecting the presence or absence of M analytes, in any combination ofpresence or absence, where M=(P*T)+1 and P is the number of codes pertier. In some examples, when degeneracy is eliminated, the method iscapable of unambiguously detecting the presence or absence of Manalytes, in any combination of presence or absence, where M=C*log₂(F+1), C is the number of second values in the coding scheme, and F isthe maximum cumulative value of the first component of the signal, forany second value, when all of the analytes are present.

This disclosure also provides non-degenerate coding schemes capable ofunambiguously encoding the presence or absence of each of at least 7analytes, in any combination of presence or absence, in a single samplevolume without immobilization, separation, mass spectrometry, or meltingcurve analysis.

In some examples, a non-degenerate coding scheme of this disclosure isgenerated by a method comprising: (a) generating a code for eachpotential analyte, wherein each potential analyte is encoded by at leastone value of at least one component of a signal; (b) enumerating everylegitimate cumulative result for all possible combinations of presenceor absence of each analyte; (c) identifying each legitimate result thatis degenerate; and (d) eliminating at least one code to eliminatedegeneracy. In some cases, the coding scheme may be expanded by addingadditional codes that are at least one unit greater than the sum of allprevious codes in the at least one component of said signal. In somecases a coding scheme is generated by a method of mathematical iterationthat guarantees non-degeneracy by construction.

In some cases, this disclosure provides systems for detecting thepresence or absence of each analyte of a plurality of analytes,comprising: (a) encoding each of said analytes as a first value of asignal, thereby generating a coding scheme, wherein each of saidanalytes is represented in said coding scheme by said first value,wherein said encoding is performed in a manner that eliminatesdegeneracy; (b) providing a sample comprising, or potentiallycomprising, at least one of said analytes; (c) contacting said samplewith analyte-specific reagents that generate said first value, asrepresented in said coding scheme, when each of said analytes ispresent; (d) cumulatively measuring said first values of said signalwithin said sample, thereby providing a cumulative measurement; and (e)determining whether each of said analytes is present or absent based onsaid cumulative measurement and said coding scheme.

In some cases, this disclosure provides systems for detecting thepresence or absence of each analyte of a plurality of analytes,comprising: (a) encoding each of said analytes as at least one firstvalue and at least one second value, wherein said first value is a valuefrom a first component of a signal and said second value is a value froma second component of said signal, thereby generating a coding scheme,wherein each of said analytes is represented in said coding scheme bysaid at least one first value and said at least one second value,wherein said encoding is performed in a manner that reduces oreliminates degeneracy; (b) providing a sample comprising, or potentiallycomprising, at least one of said analytes; (c) contacting said samplewith analyte-specific reagents that generate said at least one firstvalue and said at least one second value, as represented in said codingscheme, when each of said analytes is present; (d) cumulativelymeasuring said first values and said second values within said sample,thereby providing a cumulative measurement; and (e) determining whethereach of said analytes is present or absent based on said cumulativemeasurement and said coding scheme, wherein, when degeneracy iseliminated, said system is capable of unambiguously detecting thepresence or absence of each of at least six analytes in a single volume,in any combination of presence or absence, when each of said reagentsgenerates only one second value.

In some cases, this disclosure provides methods of detecting thepresence or absence of each analyte of a plurality of analytes for athird party, comprising: (a) obtaining the identity of each of saidanalytes from a party; (b) encoding each of said analytes as a firstvalue of a signal, thereby generating a coding scheme, wherein each ofsaid analytes is represented in said coding scheme by said first value,wherein said encoding is performed in a manner that eliminatesdegeneracy; (c) providing said party with analyte-specific reagents thatgenerate said first value, as represented in said coding scheme, wheneach of said analytes is present, said party: (i) contacting a samplecomprising, or potentially comprising, at least one of said analyteswith said reagents; and (ii) cumulatively measuring said first valueswithin said sample, thereby providing a cumulative measurement; and (d)obtaining said cumulative measurement from said party; (e) determiningwhether each of said analytes is present or absent based on saidcumulative measurement and said coding scheme; and (f) providing saidparty with information about the presence or absence of each of saidanalytes.

In some cases, this disclosure provides methods of detecting thepresence or absence of each analyte of a plurality of analytes for athird party, comprising: (a) obtaining the identity of each of saidanalytes from a party; (b) encoding each of said analytes as at leastone first value and at least one second value, wherein said first valueis a value from a first component of a signal and said second value is avalue from a second component of said signal, thereby generating acoding scheme, wherein each of said analytes is represented in saidcoding scheme by said at least one first value and said at least onesecond value, wherein said encoding is performed in a manner thatreduces or eliminates degeneracy; (c) providing said party withanalyte-specific reagents that generate said at least one first valueand said at least one second value, as represented in said codingscheme, when each of said analytes is present, said party: (i)contacting a sample comprising, or potentially comprising, at least oneof said analytes with said reagents; and (ii) cumulatively measuringsaid first values and said second values within said sample, therebyproviding a cumulative measurement; and (d) obtaining said cumulativemeasurement from said party; (e) determining whether each of saidanalytes is present or absent based on said cumulative measurement andsaid coding scheme; and (f) providing said party with information aboutthe presence or absence of each of said analytes.

In some cases, this disclosure provides compositions for detecting thepresence or absence of each analyte of a plurality of analytes,comprising analyte-specific reagents, each reagent generating a signalcomprising a first value, wherein said reagents are capable ofunambiguously detecting the presence or absence of each of at leastseven analytes in a single sample volume, in any combination of presenceor absence, without immobilization, separation, mass spectrometry, ormelting curve analysis.

In some cases, this disclosure provides compositions for detecting thepresence or absence of each analyte of a plurality of analytes,comprising analyte-specific reagents, each reagent generating a signalcomprising at least one first value that is a value from a firstcomponent of said signal and at least one second value that is a valuefrom a second component of said signal, wherein said reagents arecapable of detecting the presence or absence of each of at least sixanalytes in a single volume, in any combination of presence or absence,when each of said reagents generates only one second value.

In some cases, this disclosure provides kits for detecting the presenceor absence of each analyte of a plurality of analytes, comprisinganalyte-specific reagents, packaging, and instructions, each reagentgenerating a signal comprising a first value, wherein said kit iscapable of unambiguously detecting the presence or absence of each of atleast seven analytes in a single sample volume, in any combination ofpresence or absence, without immobilization, separation, massspectrometry, or melting curve analysis.

In some examples, this disclosure provides kits for detecting thepresence or absence of each analyte of a plurality of analytes,comprising analyte-specific reagents, packaging, and instructions, eachreagent generating a signal comprising at least one first value that isa value from a first component of said signal and at least one secondvalue that is a value from a second component of said signal, whereinsaid kit is capable of detecting the presence or absence of each of atleast six analytes in a single volume, in any combination of presence orabsence, when each of said reagents generates only one second value.

In some cases, this disclosure provides kits for detecting the presenceor absence of each analyte of a plurality of analytes, comprising a kitbody (601), clamping slots arranged in the kit body for placing bottles,a bottle comprising probes for the detection of an analyte (602), abottle comprising primers for amplification (603), and a bottlecomprising reagents for amplification (604), wherein said kit is capableof unambiguously detecting the presence or absence of each of at leastseven analytes in a single sample volume, in any combination of presenceor absence, without immobilization, separation, mass spectrometry, ormelting curve analysis.

In some examples, this disclosure provides kits for detecting thepresence or absence of each analyte of a plurality of analytes, a kitbody (601), clamping slots arranged in the kit body for placing bottles,a bottle comprising probes for the detection of an analyte (602), abottle comprising primers for amplification (603), and a bottlecomprising reagents for amplification (604), each probe generating asignal comprising at least one first value that is a value from a firstcomponent of said signal and at least one second value that is a valuefrom a second component of said signal, wherein said kit is capable ofdetecting the presence or absence of each of at least six analytes in asingle volume, in any combination of presence or absence, when each ofsaid probes generates only one second value.

INCORPORATION BY REFERENCE

All publications and patent applications mentioned in this specificationare herein incorporated by reference to the same extent as if eachindividual publication or patent application was specifically andindividually indicated to be incorporated by reference.

BRIEF DESCRIPTION OF THE DRAWINGS

The novel features of the invention are set forth with particularity inthe appended claims. A better understanding of the features andadvantages of the present invention will be obtained by reference to thefollowing detailed description that sets forth illustrative embodiments,in which the principles of the invention are utilized, and theaccompanying drawings of which:

FIG. 1 shows a comparison between a traditional encoding method ofdetecting four analytes with four colors and an encoding method of theinvention able to detect 16 or more sequences with four colors. Colorsare indicated by B, G, Y, and R, which indicate blue, green, yellow, andred, respectively.

FIG. 2 shows a schematic representation of detection of six analytes(including control) with four colors. The analytes are detected usinghybridization probes attached to a fluorophore (B, G, Y, R; blue, green,yellow, and red, respectively) and a quencher (oval with “X”). Thecontrol sequence and the five other sequences (Dengue Fever=denguevirus; Tuberculosis=Mycobacterium tuberculosis; P17=HIV p17;Malaria=Plasmodium falciparum; and Herpes=herpes simplex virus 2) areall detected using a probe labeled with a blue fluorophore. Thenon-control analytes are each detected using 1-3 additional probes. Forexample, the dengue virus analyte is detected using three additionalprobes with green, yellow, and red fluorophores; the herpes simplexvirus 2 analyte is detected using one additional probe with a redfluorophore; and so on.

FIG. 3 shows chromatograms of experimental results obtained as describedin Example 2.

FIG. 4 shows an exemplary embodiment of the invention in which acomputer is used to perform one or more steps of the methods providedherein.

FIG. 5 shows a schematic of two different methods of detectingwavelength and intensity of a light signal, such as a fluorescenceemission signal.

FIG. 6 shows a schematic of exemplary kits.

FIG. 7 shows chromatograms of experimental results obtained as describedin Example 3.

FIG. 8 shows a schematic of a legitimate result (top) and anillegitimate result (bottom).

DETAILED DESCRIPTION OF THE INVENTION

Fluorescence detection has been a preferred technique for multiplexedassays because of several desirable features, including compatibilitywith biochemical assays, the relatively small size of fluorescentlabels, simple means of conjugation to molecules of interest,affordability, low toxicity, stability, robustness, detectability withinexpensive optics, and an ability to be combined with spatial arrays.However, standard fluorophores have wide emission spectra. Therefore, inorder to avoid spectral overlap (i.e., to preserve spectral resolution)only a relatively small number of colors (e.g., 4 to 6) are typicallyused simultaneously in multiplexed fluorescent assays.

The traditional encoding method for multiplexed fluorescent assays hasbeen to encode each analyte with a single color; i.e., M=N, where M isthe number of analytes that can be detected and N is the number ofspectrally resolved fluorescent probes. Whenever higher factors ofmultiplexing are required (i.e., M>N), fluorescence is generallycombined with other techniques, such as aliquoting, spatial arraying, orsequential processing. These additional processing steps arelabor-intensive and frequently require relatively expensive and complexoptical and mechanical systems (e.g., spectrometers, mechanizedmicroscopy stages, microfluidics, droplet generators, scanners, and thelike). Such systems are often impractical to deploy in certain settings,particularly point-of care and low-resource settings. Thus, there is asignificant need for multiplexed encoding and decoding methods that canprovide an inexpensive means of multiplexing while avoiding the use ofexpensive additional processing steps.

This disclosure provides methods, systems, compositions, and kits forthe detection of multiple analytes in a sample. Analytes are detectedbased on the encoding, analysis, and decoding methods presented herein.In some examples, each analyte to be detected is encoded as a value of asignal (e.g., intensity), where the values are assigned so that theresults of the assay unambiguously indicate the presence or absence ofthe analytes being assayed. In other examples, each analyte to bedetected is encoded as a value in each of at least two components of asignal (e.g., intensity and wavelength). The at least two components ofa signal may be orthogonal. Similarly, as described more fully elsewherein this disclosure, multiple orthogonal signals may be used, such as acombination of a fluorescent signal and an electrochemical signal. Theanalyte may be any suitable analyte, such as a polynucleotide, aprotein, a small molecule, a lipid, a carbohydrate, or mixtures thereof.The signal may be any suitable signal such as an electromagnetic signal,a light signal, a fluorescence emission signal, an electrochemicalsignal, a chemiluminescent signal, and combinations thereof. The atleast two components of the signal may be any suitable two components,such as an amplitude and a frequency or an intensity and a wavelength.

After encoding of the analytes, a sample is provided wherein the samplecomprises or may comprise at least one of the encoded analytes. Thesample is contacted with an analyte-specific reagent or reagents thatgenerate a particular signal, as specified for each analyte in thecoding scheme, in the presence of an analyte. A reagent may be anysuitable reagent that is capable of generating such a signal in thepresence of its corresponding analyte, for example, an oligonucleotideprobe attached to a fluorophore and a quencher (e.g., a TAQMAN probe).If the reagent is an oligonucleotide probe attached to a fluorophore anda quencher, a nucleic acid amplification may be performed to generatethe signal.

After addition of the reagent(s), the signal is quantified. In somecases, this quantification is performed by measuring one component ofthe signal (e.g., fluorescence intensity) and determining the presenceand absence of certain analytes based on the values used to encode thepresence of each analyte and the cumulative value of the signal.

In some cases, at least two components of a signal (e.g., intensity andwavelength) are cumulatively measured for the sample. This measurementcan be performed, for example, by measuring the intensity at aparticular wavelength or the intensity within a particular range ofwavelengths. The presence or absence of an analyte may then bedetermined based on the values of each of the at least two components ofthe signal and the values used to encode the presence of the analyte(i.e., those values in the coding scheme).

The encoding may be performed in a manner that reduces or eliminates thenumber of possible degenerate (e.g., ambiguous) results that can beobtained by the method. As described elsewhere in this specification,the full coding capability of a particular coding scheme may beenumerated, and certain potential analyte codes may be eliminated fromthe coding scheme to reduce or eliminate degeneracy. Similarly, a codingscheme may be designed to be non-degenerate, so that a reduction orelimination of degeneracy is not necessary. A decoding matrix may beconstructed to translate cumulative signal measurements (e.g.,intensities or intensities at particular wavelengths) into the presenceor absence of certain analytes, corresponding to the constituent signalsof the cumulative signal measurement.

I. Definitions

The terminology used herein is for the purpose of describing particularembodiments only and is not intended to be limiting.

As used herein, the singular forms “a,” “an,” and “the” are intended toinclude the plural forms as well, unless the context clearly indicatesotherwise. Furthermore, to the extent that the terms “including,”“includes,” “having,” “has,” “with,” “such as,” or variants thereof, areused in either the specification and/or the claims, such terms are notlimiting and are intended to be inclusive in a manner similar to theterm “comprising”.

The term “about,” as used herein, generally refers to a range that is15% greater than or less than a stated numerical value within thecontext of the particular usage. For example, “about 10” would include arange from 8.5 to 11.5.

The terms “dimension” and “component,” as used herein when referring toa signal, generally refer to an aspect of the signal that may bequantified. For example, if a signal is generated by a fluorescentmolecule, it may be quantified in terms of its wavelength (e.g., a firstdimension or component) and its intensity (e.g., a second dimension orcomponent).

The term “decoding,” as used herein, generally refers to a method ofdetermining which analytes are present based on the cumulative signaland a coding scheme or decoding matrix that enables the conversion of acumulative signal to information concerning the presence or absence ofone or more analytes.

The term “encoding,” as used herein, generally refers to the process ofrepresenting an analyte using a code comprising values of a signal, suchas intensity, or values in each of at least two components of a signalor signals, such as wavelength and intensity.

The terms “oligonucleotide probe attached to a fluorophore and aquencher” and “TAQMAN probe” generally refer to hydrolysis probes usedto detect the presence of an analyte in a polynucleotide amplificationassay. These probes comprise an oligonucleotide probe attached to afluorophore and a quencher. So long as the quencher and the fluorophoreare in proximity, the quencher quenches the fluorescence emitted by thefluorophore upon excitation by a light source. The sequence of theoligonucleotide probe is designed to be complementary to apolynucleotide sequence present in an analyte, and therefore capable ofhybridizing to the polynucleotide sequence present in the analyte.Hybridization of the oligonucleotide probe is performed in a nucleicacid amplification reaction comprising primers (e.g., a polymerase chainreaction). Upon extension of the primers by a DNA polymerase, the 5′ to3′ exonuclease activity of the polymerase degrades the probe, releasingthe fluorophore and the quencher into the medium. The proximity betweenthe fluorophore and the quencher is broken and the signal from thefluorophore is no longer quenched. Thus, the amount of fluorescencedetected is a function of the amount of analyte present. If no analyteis present, the probe will not hybridize to an analyte, and thefluorophore and quencher will remain in close proximity. Little or nosignal will be produced.

The term “orthogonal,” as used herein, generally refers to at least twocomponents of a signal (e.g., wavelength and intensity), or at least twodifferent signals (e.g., fluorescence emission and electrochemicalsignal), that can be varied independently or approximatelyindependently. For example, wavelength and intensity are consideredorthogonal or approximately orthogonal when fluorescent molecules areused. Among other factors, the wavelength of fluorescence emission willdepend on the composition of the fluorescent molecule and the intensityof the fluorescence will depend on the amount of molecule present.Although wavelength and intensity are examples of two components of asignal that can be varied approximately independently, the methodsdescribed herein are not limited to components that can be variedindependently or approximately independently. Components of a signal, orsignals, that vary non-independently may also be used, so long as thecomponents or signals are characterized well enough to enable encoding,measurement, and decoding. For example, if the variance in one componentor signal affects the variance in another component or signal, the twocomponents or signals may still be used so long as the relationshipbetween the variances is understood.

The terms “polynucleotide,” “oligonucleotide,” or “nucleic acid,” asused herein, are used herein to refer to biological molecules comprisinga plurality of nucleotides. Exemplary polynucleotides includedeoxyribonucleic acids, ribonucleic acids, and synthetic analoguesthereof, including peptide nucleic acids.

The term “probe,” as used herein, generally refers to a reagent capableof generating a signal in the presence of a particular analyte. A probegenerally has at least two portions: a portion capable of specificallyrecognizing an analyte, or a portion thereof, and a portion capable ofgenerating a signal in the presence of an analyte, or a portion thereof.A probe may be an oligonucleotide probe attached to a fluorophore and aquencher, as described above and elsewhere in this disclosure. A probemay also be any reagent that generates a signal in the presence of ananalyte, such as an antibody that detects an analyte, with a fluorescentlabel that emits or is quenched upon binding of the antibody to ananalyte. Any suitable probe may be used with the methods presented inthis disclosure, so long as the probe generates a quantifiable signal inthe presence of an analyte. For example, the analyte-specific portion ofa probe may be coupled to an enzyme that, in the presence of an analyte,converts an uncharged substrate into a charged product, therebyincreasing the electrical conductivity in the medium over time. In thiscase, different analytes may be encoded by coupling the analyte-specificportion of the probe (e.g., hybridization probe or antibody) to anenzyme at different ratios. The resulting rate of increased conductivityin the medium will be cumulative for all analytes present in the medium.Encoding analytes according to the methods provided herein enablesconversion of the conductivity measurements into unambiguous (i.e.,non-degenerate) results providing information about the presence orabsence of particular analytes. Similarly, a probe may comprise anenzyme producing a chemiluminescent product from a substrate. The amountof chemiluminescence may then be used to encode the presence ofparticular analytes.

II. Encoding and Decoding Methods

A. Traditional Fluorescent Encoding and Decoding Method

A commonly used method of determining the presence of an analyte usesfour spectrally resolved fluorescent molecules to indicate the presenceor absence of four analytes. An example of this method is presented onthe left-hand side of FIG. 1 . The left-hand side of FIG. 1 shows anencoding method where four analytes (Seq 1, Seq 2, Seq 3, and Seq 4) areeach encoded by a single color (blue, green, yellow, and red,respectively). The color represents a fluorophore attached to anoligonucleotide probe that also comprises a quencher. In the systemshown on the left-hand side of FIG. 1 , there are four differentoligonucleotide probes, each comprising a single fluorophore (blue,green, yellow, or red) and a quencher. The presence or absence of ananalyte is determined based on the presence or absence of a signal in aparticular color.

The chart on the left-hand side of FIG. 1 shows intensity versus colorfor a hypothetical sample containing two analytes: Seq 1 and Seq 3. Thepresence of these analytes is determined based on the measurement of ablue signal (corresponding to Seq 1) and a yellow signal (correspondingto Seq 3). The absence of Seq 2 and Seq 4 is indicated by the absence ofa blue and red signal.

Table 1 shows a translation of this coding scheme into a binary format.Each analyte is encoded as a value in each of two components of afluorescent signal: (1) color (also known as wavelength; or range ofwavelengths) and (2) intensity (indicated by the numbers within thetable). For example, A (e.g., Seq 1) has a color of blue and anintensity of 1; B (e.g., Seq 2) has a color of green and an intensity of1; and so on. The intensity of the signal within each color range may bequantified as described herein, for example by measuring the intensityof the signal within a particular wavelength range determined by a bandpass filter. A result of 1000 indicates that only analyte A is present;a result of 1100 indicates that analytes A and B are present; and so on.

TABLE 1 Traditional encoding of four analytes with four probes, eachprobe having a single color, and one probe per analyte. Blue GreenYellow Red A 1 0 0 0 B 0 1 0 0 C 0 0 1 0 D 0 0 0 1B. Encoding Methods Using More than One Color Per Analyte

The traditional method described above suffers from the fact that it islimited by the number of spectrally resolvable fluorophores. Morespecifically, the number of detectable analytes is equal to the numberof spectrally resolvable fluorophores. Therefore, the number of analytesmay only be increased by increasing the number of spectrally resolvablefluorophores.

This disclosure provides methods that overcome this limitation. Morespecifically, in some cases, by utilizing at least two components of asignal during encoding, the methods described herein may be used todetect more than one analyte per fluorophore. For example, using themethod provided herein 1.5, 1.6, 1.7, 1.8, 1.9, 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45,46, 47, 48, 49, or 50 analytes may be detected per fluorophore. In somecases, the methods provided herein may be used to detect at least 1.5,1.6, 1.7, 1.8, 1.9, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34,35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50analytes may be detected per fluorophore. In some cases, the methodsprovided herein may be used to detect 1.5-2, 2-4, 1.5-4, 4-6, 2-6, 6-10analytes per fluorophore.

In some cases, the methods provided in this disclosure may include theuse of a control color. The control color may be attached to one or moreprobes binding a positive control analyte, and each analyte to bedetected, in a sample. If the same sequence occurs in the positivecontrol analyte and each analyte to be detected, a single control probemay be used. If the same sequence does not occur in the positive controlanalyte and each analyte to be detected, different probes may be used,but each probe may still be attached to the control color.

For example, building on the traditional methods described above, onecolor (e.g., blue) may be used to encode the presence of a controlanalyte that is always present in the sample. The control analyte may beadded to the sample, or may be inherently present in the sample. Theremaining colors (e.g., green, yellow, red) may be used to encode thepresence of additional analytes. Table 2 shows an example of one suchmethod.

TABLE 2 Encoding of four analytes, including control, with four colorsand up to two colors per analyte. Blue Green Yellow Red Ctrl. (p) 1 0 00 A 1 0 0 1 B 1 0 1 0 C 1 1 0 0

In Table 2, the presence of the control (p) is indicated by a result of1000. The presence of the control and analyte A is indicated by a resultof 2001. The presence of the control and all three other analytes isindicated by a result of 4111. The control color (blue) provides anindication that the assay is functioning properly. The intensity of theblue color reports the number of analytes that are present in a testsample. Of course, any color may be used as the control color. One ofskill in the art will recognize that certain practical considerationsmight make it preferable to use one color over another as the controlcolor. For example, if one color is better detected in a particularoptical system (or system of fluorophores), it might be practicallypreferable to use that color as a control color.

The coding scheme shown in Table 2 encodes each analyte using onecontrol color and one additional color (up to 2 probes per analyte).However, as shown below, the number of analytes that can be encodedincreases when up to 4 colors are used per analyte. Table 3 shows anexemplary coding scheme where each analyte is encoded by up to 4 colors.In the scheme shown in Table 3, the control color (blue) is generated inthe presence of the control sequence and each of the other sevenanalytes (A-G). The other seven analytes are each encoded by thepresence of one to three additional colors. The colors may be containedon different probes (e.g., oligonucleotide probes attached to afluorophore and a quencher) or on the same probe (which can havemultiple fluorophores and multiple quenchers).

TABLE 3 Encoding of eight analytes (including control) with four colorsand up to four colors per analyte. Blue Green Yellow Red Ctrl. (p) 1 0 00 A 1 0 0 1 B 1 0 1 0 C 1 1 0 0 D 1 0 1 1 E 1 1 0 1 F 1 1 1 0 G 1 1 1 1

In Table 3, the presence of the control and all seven other analytes isindicated by a result of 8444. Three analytes (A, B, and C) are encodedby two colors. Three analytes (D, E, and F) are encoded by three colors,and one analyte (G) is encoded by four colors. The presence of thecontrol (p) is indicated by a result of 1000. The presence of thecontrol and analyte A is indicated by a result of 2001. The presence ofthe control and analyte G is indicated by a result of 2111. Theseresults express the cumulative intensity of the signal in each color.For example, the result 2111 has a 2× signal intensity in the bluechannel, while the result 1000 has only a 1× signal intensity in theblue channel.

Using Table 3, each of the possible cumulative assay results can beenumerated, in terms of color (blue, green, yellow, red) and intensity(0-8). Table 4 shows a “decoding matrix” generated by enumerating eachof the possible cumulative assay results based on the encoding methodpresented in Table 3 and providing the corresponding decoded result ofeach assay in terms of the analyte(s) present in the sample. A similardecoding matrix may be generated for any coding scheme described herein,by enumerating each of the possible cumulative assay results based onthe coding scheme and providing the corresponding decoded result of eachassay in terms of the analyte(s) present in (or absent from) the sample.In some cases, as described below, one or more analytes may be removedfrom the coding scheme in order to reduce or eliminate degeneracy.

TABLE 4 Decoding matrix for encoding method presented in Table 3.Cumulative Assay Result Blue Green Yellow Red Analyte(s) Present 1 0 0 0p 2 0 0 1 pA 2 0 1 0 pB 2 1 0 0 pC 2 0 1 1 pD 2 1 0 1 pE 2 1 1 0 pF 2 11 1 pG 3 0 1 1 pAB 3 1 0 1 pAC 3 0 1 2 pAD 3 1 0 2 pAE 3 1 1 1 pAF, pCD,pBE 3 1 1 2 pAG, pDE 3 1 1 0 pBC 3 0 2 1 pBD 3 1 2 0 pBF 3 1 2 1 pBG,pDF 3 2 0 1 pCE 3 2 1 0 pCF 3 2 1 1 pCG, pEF 3 1 2 2 pDG 3 2 1 2 pEG 3 22 1 pFG 4 1 1 1 pACB 4 0 2 2 pABD 4 2 2 0 pBCF 4 2 0 2 pACE 4 1 1 2pABE, pACD 4 1 2 1 pABF, pBCD 4 2 1 1 pACF, pBCE 4 1 2 2 pADF, pABG,pBDE 4 2 1 2 pACG, pCDE, pAEF, 4 2 2 1 pBCG, pBEF, pCDF 4 2 2 2 pCDG,pAFG, pBEG, pDEF 4 1 1 3 pADE 4 1 3 1 pBDF 4 3 1 1 pCEF 4 1 2 3 pADG 4 32 1 pCFG 4 2 1 3 pAEG 4 2 3 1 pBFG 4 1 3 2 pBDG 4 3 1 2 pCEG 4 2 2 3pDEG 4 3 2 2 pEFG 5 1 2 2 pABCD 5 2 1 2 pABCE 5 2 2 1 pABCF 5 2 2 2pABCG, pABEF, pBCDE, pACDF 5 1 2 3 pABDE 5 2 1 3 pACDE 5 1 3 2 pABDF 5 21 3 pBCDF 5 3 1 2 pACEF 5 3 2 1 pBCEF 5 2 2 3 pABEG, pACDG, pADEF 5 2 32 pABFG, pBCDG, pBDEF 5 3 2 2 pACFG, pBCEG, pCDEF 5 1 3 3 pABDG 5 3 1 3pACEG 5 3 3 1 pBCFG 5 2 3 3 pADFG, pBDEG 5 3 3 2 pBEFG, pDEFG 5 3 2 3pCDEG, pAEFG 5 2 2 4 pADEG 5 2 4 2 pBDFG 5 4 2 2 pCEFG 5 3 3 3 pDEFG 6 22 3 pABCDE 6 2 3 2 pABCDF 6 3 2 2 pABCEF 6 2 3 3 pABCDG, pABDEF 6 3 2 3pABCEG, pACDEF 6 3 3 2 pABCFG, pBCDEF 6 4 3 2 pBCEFG 6 4 2 3 pACEFG 6 33 3 pABEFG, pACDFG, pBCDEG 6 3 4 2 pBCDFG 6 2 4 3 pABDFG 6 3 2 4 pACDEG6 2 3 4 pABDEG 6 4 3 3 pCDEFG 6 3 4 3 pBDEFG 6 3 3 4 pADEFG 7 4 4 3pBCDEFG 7 4 3 4 pACDEFG 7 3 4 4 pABDEFG 7 4 3 3 pABCEFG 7 3 4 3 pABCDFG7 3 3 4 pABCDEG 7 3 3 3 pABCDEF 8 4 4 4 pABCDEFG

The decoding matrix provided in Table 4 is constructed using twoassumptions. First, the decoding matrix assumes that the positivecontrol (p) always produces a positive outcome. Second, the decodingmatrix assumes that, within each color, the intensity is additive andscales in the same way with changing probe concentration, regardless ofwhich probe the signal may come from. This essentially means that thesignals are additive and digital. The conditions underlying theseassumptions may be met by properly preparing the assay. If a fluorescentsignal is used, the intensity need only be approximately additive anddigital, as demonstrated in the Examples provided herein.

Table 4 allows the conversion of a cumulative measurement of intensityin four ranges of fluorescent wavelengths (i.e., signal intensity withineach color range), into the corresponding analytes present in thesample. For example, a result of 4321 indicates that p, C, F, and G arepresent and the other analytes are not present. This result is referredto as a “legitimate” result, because it is present in the decodingmatrix. By contrast, a result of 4000, while possible to measure, doesnot occur in the decoding matrix. More specifically, the result of 4000cannot be achieved by adding any combination of control and analytecodes from Table 3. This result is referred to as an “illegitimate”result. An illegitimate result may indicate that the assaymalfunctioned. Thus, the control (p) and the decoding matrix provide ameans of verifying that the assay is functioning properly.

Table 4 is exhaustive for any combination of fluorophores generatingfour resolvable emission spectra (e.g., colors). The term “rank” is usedto describe the number of detected analytes, including the control. Inthe example provided above, if the assay functions properly, the rank isequal to the value of the blue signal. For example, a rank of 8indicates that the control and all seven other analytes (A-G) arepresent. A rank of 2 indicates that the control and only one analyte arepresent. The lowest rank is a rank of 1, which indicates that only thecontrol is present. The number of possibilities at each rank can beenumerated. For example, continuing to refer to the encoding anddecoding method described in Tables 3-4, there are 7 possibilities forrank 2. The number of possibilities at rank 3 can be calculated as acombination of 7 take 2, or 7!/(5!*2!)=21 possibilities. More generally,the number of possibilities for a combination of N take K isN!/((N−K)!*K!). Analogously, at ranks 4, 5, 6, 7, and 8, the number ofpossibilities is 35, 35, 21, 7, and 1, respectively. Referring to Table4 shows that the table agrees with the theoretical prediction. Thus,Table 4 is an exhaustive decoding matrix for the encoding methodprovided in Table 3.

C. Reducing or Eliminating Degeneracy

The terms “degenerate” and “degeneracy,” as used herein, generallydescribe a situation where a legitimate result is not definitive,because it can indicate more than one possibility in terms of thepresence or absence of an analyte. For example, with reference to Table4, result 5233 is degenerate because it can be decoded as either pADFGor pBDEG. Similarly, result 4222 is degenerate because it can be decodedas any of the following: pCDG, pAFG, pBEG, pDEF. By contrast, result3110 can only indicate pBC and thus is not degenerate.

This disclosure provides methods of reducing or eliminating degeneracy,thereby increasing the confidence with which an analyte is detected. Inone embodiment, degeneracy is eliminated by a method comprising (i)encoding each potential analyte to be detected as a value of a signaland, optionally, as a value in each of at least two components of asignal; (ii) enumerating every legitimate result that can be obtainedfrom the coding scheme; (iii) identifying each legitimate result that isdegenerate; and (iv) eliminating at least one potential analyte (orpotential analyte code) from the coding scheme, wherein eliminating theat least one potential analyte reduces or eliminates degeneracy. Forexample, with reference to the coding scheme described in Table 3 andthe decoding matrix described in Table 4 (enumerating every legitimateresult), eliminating any two of analytes D, E, and F eliminates thedegeneracy. Eliminating any one of analytes D, E, and F would noteliminate the degeneracy, but would reduce it.

With continued reference to the coding scheme described in Table 3,eliminating any two of analytes D, E, and F from the coding schemeresults in a scheme where six analytes (including control) can beanalyzed, with no degeneracy, using only 4 colors. By contrast,conventional methods of multiplexing would allow for only the reportingof 3 analytes and 1 control using 4 colors. Therefore, the number ofanalytes that can be analyzed is nearly doubled by using the methodsprovided herein.

FIG. 2 shows an exemplary embodiment of the invention in which 4 colorsare used to detect five analytes and a control. The analytes are nucleicacids from dengue virus (“Dengue Fever”), Mycobacterium tuberculosis(“Tuberculosis”), human immunodeficiency virus (HIV) p17 (P17),Plasmodium (“Malaria”), and herpes simplex (“Herpes”). The “colors” inthis example are fluorophores attached to oligonucleotide probes thatalso comprise a quencher. The oligonucleotide probes will generally bedifferent for different analytes, whereas the color is the same. Forexample, all probes designated as Probe 1 have a blue color butgenerally will have a different oligonucleotide sequence. Of course,probes designated as Probe 1 could also have the same oligonucleotidessequence, if the complementary sequence was present in each of theanalytes. The mechanism of detection with these probes is describedelsewhere in this disclosure. Probe 1 (blue) hybridizes to all sixanalytes, including control. Probe 2 (green) hybridizes to analytes fromdengue virus, Mycobacterium, and HIV p17. Probe 3 (yellow) hybridizes toanalytes from dengue fever and Plasmodium. Probe 4 hybridizes toanalytes from dengue virus, Mycobacterium, and herpes simplex. Thecoding scheme defined by these probes is illustrated in Table 5. Withreference to Table 3, potential analytes D (1011) and F (1110) have beeneliminated from the coding scheme. Therefore, the coding schemepresented in Table 5 is non-degenerate and each legitimate result fromthe assay corresponds to the presence or absence of a unique combinationof analytes in a sample.

TABLE 5 Coding scheme for detection of dengue virus, Mycobacterium, HIV,Plasmodium, and herpes simplex, as exemplified in FIG. 2. Blue GreenYellow Red Ctrl. (p) 1 0 0 0 Herpes Simplex 1 0 0 1 Plasmodium 1 0 1 0HIV 1 1 0 0 Mycobacterium 1 1 0 1 Dengue Virus 1 1 1 1

The methods for encoding and decoding presented above, including themethods for eliminating degeneracy, are all equally applicable toencoding methods using additional colors. For example, Table 3 could beextended by including additional colors and additional intensities(described further below). The decoding matrix is then generated asdescribed above, enumerating every legitimate result that can beobtained from the coding scheme. A decoding matrix analogous to thedecoding matrix provided in Table 4 may be constructed for any codingscheme described in this disclosure. The legitimate results that aredegenerate are then identified and at least one potential analyte codeis eliminated from the coding scheme to reduce or eliminate degeneracy.The method of eliminating degeneracy may be carried out using softwareon a computer readable medium, or hardware configured to carry out themethod (e.g., a microchip).

Although degeneracy can be reduced or eliminated by the methodsdescribed above, and elsewhere in this disclosure, this disclosure alsoprovides coding schemes that are non-degenerate by design. For example,after elimination of degeneracy in the coding scheme described in Table3, the coding scheme may be extended indefinitely in a non-degeneratemanner where the non-degeneracy is by design (see, e.g., the codingscheme exemplified in Table 6, described more fully below). Similarly,this disclosure provides coding schemes that are completelynon-degenerate by design and therefore do not require any reduction orelimination of degeneracy (see, e.g., the coding scheme exemplified inTable 8, described more fully below). Thus, the coding schemes providedin this disclosure may have reduced or eliminated degeneracy, or benon-degenerate by design.

D. Encoding Methods Using More than One Color and More than OneIntensity

The encoding method described above (e.g., Tables 3-5) may be furtherextended by allowing analytes to be encoded by an intensity greaterthan 1. For example, each of the analytes encoded in the coding schemeprovided in Table 5 is encoded by a fluorescence intensity of either 1or 0. Allowing higher values for the signal intensity in at least onecolor further increases the number of analytes that can be encoded byany of the methods provided in this disclosure. In some examples, thesehigher intensity values may be assigned any color except for the controlcolor, in order to maintain the analyte counting capability of thecontrol color.

Table 6 shows the first three tiers of an exemplary coding scheme thatutilizes four colors and multiple intensities. Tier 1 of Table 6 is areproduction of Table 3, showing the encoding of seven analytes and acontrol with four colors. As described above, any two of potentialanalytes D, E, and F may be eliminated from the coding scheme in orderto produce a non-degenerate coding scheme. Tier 1 of Table 6 indicatesthat potential analytes D (1011) and F (1110) have been eliminated fromthe coding scheme to eliminate degeneracy. Therefore, the coding schemepresented in Tier 1 of Table 6 is capable of determining the presence offive analytes and one control using four colors, as described above.

The coding scheme of Tier 1 of Table 6 may be expanded to a second tier(Tier 2) by allowing the intensity in any of the colors to increase. Asdescribed above, the intensity of the control color may be maintained at1, in order to preserve the sequence counting capability of the control.Increasing the intensity of any of the remaining three colors will yieldcodes 100Y, 10Y0, 1Y00, 10YY, 1Y0Y, 1YY0, and 1YYY, where Y>1. Theminimal value of Y for a new tier of encoding is equal to the cumulativemaximum value from the prior tier(s) plus 1. As described below, a valuegreater than 1 could also be used, to maximize the differences betweenthe intensities.

Thus, in this context, the term “tier” is generally used to describe aset of codes that fully utilize the coding capability provided by aparticular number of first values (e.g., intensities) and second values(e.g., colors), without degeneracy. For example, Tier 1 of Table 6 fullyutilizes the coding capability provided by four colors with up to oneintensity in each color, without degeneracy. As shown in Table 6, Tier1, this results in six encoded analytes, including the control. Tointroduce a second tier, the minimum value of Y (described above) may beincremented to equal the cumulative maximum result from the priortier(s) plus one (or more than one). In the example provided in Table 6,the intensity of the blue (control) color is maintained as one, topreserve the sequence counting capability in this color. Thus, Tier 2consists of five non-degenerate encoding possibilities obtained byincrementing the intensities in the green, yellow, and red channels toequal the cumulative maximum results in each of these channels from Tier1, plus one. All possibilities of these codes may then be enumerated forTier 2, and codes resulting in degeneracy may be eliminated, or Tier 2may be made non-degenerate by design, using the information used toeliminate the corresponding codes from Tier 1. Further coding capacitymay then be achieved by adding a third tier, or further tiers, which areconstructed according to analogous methods. A coding scheme may have aninfinite number of tiers, for example 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29,30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50, 60, 70, 80, 90, 100 or more tiers.

More specifically, with reference to Table 6, Tier 2, analyte H isencoded by 1004. The value of the control color is maintained as 1. Thevalue of the red color is equal to the cumulative maximum result fromthe prior tier (3) plus 1, or 4. Similarly, analytes I and J are encodedby 1030 and 1400, respectively. Combinations of these codes are used toencode the remaining four analytes (K-N), as was done for analytes D-Gin Tier 1. This completes Tier 2. In Tier 2, the inclusion of potentialanalytes K (1034) and M (1430) results in degeneracy. Therefore, theseanalytes have been eliminated from the coding scheme, to eliminatedegeneracy.

Continuing to refer to Table 6, a third tier (Tier 3) is constructedusing the same principles described above. Analyte 0 is encoded by1-0-0-16. The value of the control color is still maintained as 1. Thevalue of the red color is equal to the cumulative maximum result fromthe prior tiers (15) plus 1, or 16. Similarly, analytes P and Q areencoded by 1-0-9-0 and 1-16-0-0, respectively. Combinations of thesecodes are used to encode the remaining four analytes (R-U), as was donefor analytes D-G in Tier 1 and analytes K-N in Tier 2. In Tier 3, theinclusion of potential analytes R (1-0-9-16) and T (1-16-9-0) results indegeneracy. Therefore, these analytes have been eliminated from thecoding scheme, to eliminate degeneracy.

The three-tier coding scheme shown in Table 6 shows the encoding of 15analytes and one control using four colors. This coding scheme may beindefinitely extended, by adding more intensities to generate additionaltiers and/or adding more colors, to generate additional codingcapability within the tiers. The methods of reducing or eliminatingdegeneracy, as described in this disclosure, may be used with theaddition of each intensity and/or color, to reduce or eliminatedegenerate results.

More generally, the coding scheme depicted in Table 6 is anon-degenerate, infinite extension of the coding scheme depicted inTables 3-5. The maximum intensity of the cumulative measurement at thefirst tier is 6. The maximum intensity of the cumulative measurement atthe second tier is 15. The maximum intensity of the cumulativemeasurement at the third tier is 63, and so on. Given a maximumcumulative intensity value (F), the maximum number of tiers (7)available in this coding scheme is T=logo (F+1). The coding schemedepicted in Table 6 provides five non-degenerate codes per tier (P).Thus, the maximum number of codes M=5*log₄ (F+1), or M=P*T, where P isthe number of non-degenerate codes per tier and T is the number oftiers. For example, given F=63, the maximum number of codes (i.e.,analytes) is 15 for 5 non-degenerate codes per tier. This formula doesnot include the 1000 code, which is reserved for a positive control inTable 6. To include the control in the total number of analytes, onewould simply add one, to provide the formula M=(P*T)+1.

The methods provided in this disclosure may be used to expand thiscoding scheme infinitely. For example, by utilizing combinations ofdifferent intensities (i.e., first values) and colors (i.e., secondvalues) one can encode any number of analytes (M) by varying the numberof non-degenerate codes per tier (P) and the number of tiers (T). Forexample, the number of non-degenerate codes per tier is 1, 2, 3, 4, 5,6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42,43, 44, 45, 46, 47, 48, 49, 50, 60, 70, 80, 90, 100, or more. Similarly,the number of tiers may be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,50, 60, 70, 80, 90, 100, or more.

TABLE 6 Encoding of 15 analytes and one control using four colors andmultiple intensities. Tier Analyte B G Y R Comments 1 Ctrl. (p) 1 0 0 0A 1 0 0 1 B 1 0 1 0 C 1 1 0 0

Eliminated from coding scheme to eliminate degeneracy. E 1 1 0 1

Eliminated from coding scheme to eliminate degeneracy. G 1 1 1 1Cumulative 6 3 2 3 Maximum Result 2 H 1 0 0 4 I 1 0 3 0 J 1 4 0 0

4 Eliminated from coding scheme to eliminate degeneracy. L 1 4 0 4

4

Eliminated from coding scheme to eliminate degeneracy. N 1 4 3 4Cumulative 11  15  8 15  Maximum Result 3 O 1 0 0 16  P 1 0 9 0 Q 1 16 0 0

  Eliminated from coding scheme to eliminate degeneracy. S 1 16  0 16 

 

Eliminated from coding scheme to eliminate degeneracy. U 1 16  9 16 Cumulative Maximum Result Cumulative 16  63  26  63  Maximum Result forThree Non- Degenerate Tiers

The right-hand side of FIG. 1 shows one exemplary embodiment of themethod described above. More specifically, the right-hand side of FIG. 1shows an encoding method where nine or more analytes (Seq 1-Seq 9, etc.)are each encoded by at least two colors, with varying intensities withineach color. The color represents a fluorophore attached to anoligonucleotide probe that also comprises a quencher. The system can bedesigned so that each probe is labeled with single fluorophore, or eachprobe is labeled with more than one fluorophore. For example, the codefor analyte H, in Table 6, is 1004. The intensity of 4 in the redchannel may be achieved by either using an H-specific probe comprising 4red fluorophores, or by using 4 H-specific probes each comprising asingle red fluorophore. Of course, any combination of probes andfluorophores producing a result of 4 in the red channel would be equallyappropriate, such as 2 probes with 2 red fluorophores each, and 1 probewith 1 red fluorophore and 1 probe with 3 red fluorophores, or simplyone probe with one red fluorophore but present at 4× amount in thereaction mixture.

The coding scheme depicted on the right-hand side of FIG. 1 may berepresented as in Table 7. The result of the analysis shown on theright-hand side of FIG. 1 is 4112, or an intensity of 4 in the bluechannel, 1 in the green channel, 1 in the yellow channel, and 2 in thered channel. Using a decoding matrix constructed as described herein,this result is decoded to indicate the presence of Seq 1, Seq 3, Seq 4,and Seq 5.

TABLE 7 Coding scheme illustrated on the right-hand side of FIG. 1. TierAnalyte B G Y R Comments 1 Seq 1 1 0 0 0 Seq 2 1 1 0 0 Seq 3 1 0 1 0 Seq4 1 0 0 1 Seq 5 1 1 0 1 Seq 6 1 1 1 1

Eliminated from code scheme to eliminate degeneracy.

Eliminated from coding scheme to eliminate degeneracy. Cumulative 6 3 23 Maximum Result 2 Seq 7 1 4 0 0 Seq 8 1 0 3 0 Seq 9 1 0 0 4 Etc. -i.e.Continue as provided in Table 6.E. Encoding Methods Using One Color and One Intensity Per Analyte butDifferent Intensities Among Analytes

In some methods provided herein, each analyte is encoded by a singlecolor and intensity combination. For example, in a four color system,the first four analytes may be encoded by 1000, 2000, 4000, and 8000.The next four analytes may be encoded by 0100, 0200, 0400, and 0800.Analytes 9-12 and 13-16 would be assigned analogously, as shown in Table8.

Like the encoding method described in Table 6, this coding scheme istheoretically infinite, non-degenerate by construction, and only limitedby the bandwidth of the instrument used to measure the signal. However,this coding scheme enables more analytes to be quantified per unit ofbandwidth than the encoding method described in Table 6. The reason isthat the available multiplicity of signal is used with maximalefficiency, as each level of intensity is utilized in the coding (i.e.there are no gaps in the chromatogram; see below for description ofchromatograms). Table 8 shows one embodiment of this method,illustrating four tiers of encoding based on four colors and intensities1, 2, 4, and 8. The coding scheme is non-degenerate, and the result ifall 16 analytes are present is 15-15-15-15. This encoding method is moreefficient, in terms of bandwidth utilization, than the encoding methodspresented above. However, this method does not have the proofreadingcapability of the first scheme, as all the results decode to legitimateoutcomes in the absence of gaps in the chromatogram.

TABLE 8 Example of encoding method using one color and one intensity peranalyte, but different intensities among analytes. Tier Analyte B G Y R1 A 1 0 0 0 B 2 0 0 0 C 4 0 0 0 D 8 0 0 0 2 E 0 1 0 0 F 0 2 0 0 G 0 4 00 H 0 8 0 0 3 I 0 0 1 0 J 0 0 2 0 K 0 0 4 0 L 0 0 8 0 4 M 0 0 0 1 N 0 00 2 0 0 0 0 4 P 0 0 0 8 15 15 15 15

The method presented above, and exemplified in Table 8, may be extendedby introducing additional colors and/or intensities. For example, 5, 6,7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,44, 45, 46, 47, 48, 49, 50, 60, 70, 80, 90, 100, or more colors may beused. Additional intensity levels, such as 16, 32, 64, 128, 255, 512,1024, 2048, 4096, 8192, 16384, 32768, 65536, and so on may also be used.The method is generalizable and may be used to encode an infinite numberof analytes. Each analyte is represented by a code in a single color,wherein the value of the code in that single color equal to the sum ofall previous values plus one. For example, if the first code contains a1 in a particular color, the next codes are 2, 4, 8, 16, 32, 64, 128 andso on. Other progressions are possible, but will not be as efficient interms of usage of the bandwidth. However, one of ordinary skill in theart will recognize that less efficient use of bandwidth may be desirablewhen one wishes to maximize separation between values. Similarly, thevalue 1 could be excluded from the coding scheme, for example tomaximize the difference in the intensity between the first encoded valueand instrumental noise. For example, in some cases a coding scheme maybegin with a value of 2, which would provide a progression of 2, 4, 8,16, 32, 64, 128, and so on for the analyte codes, while the progressionof cumulative results would be 2, 4, 6, 8, 10, 12, 14, 16, and so on.This approach generates uniform gaps in the possible cumulative results,allowing for higher tolerance to noise in comparison to an analyte codeprogression of 1, 2, 4, 8, 16, 32, and so on, and its correspondingcumulative result progression of 1, 2, 3, 4, 5, 6, 7, 8, and so on. Inthis example, the increased robustness in the measurement comes at acost of a decrease in the number of available codes within a fixedbandwidth of multiplicity. For example, if only 63 multiplicity statescan be measured reliably, the coding scheme starting with 1 offers 7codes per color whereas the coding scheme starting with 2 offers 6 codesper color. If 4 colors are available, the former will offer 28 codes,while the latter will offer 24 codes. In summary, both the startingsignal intensity and the progression (i.e., difference between intensityvalues) may be scaled in order to maximize the ability to distinguishover instrumental noise and maximize the differences between theintensity values, thereby enhancing the ability to distinguish betweendistinct experimental outcomes.

The coding scheme illustrated in Table 8 is non-degenerate by design.Although the coding scheme illustrated in Table 8 uses both intensityand color to encode each of the 16 analytes, each of the analytes couldalso be encoded by simply utilizing intensity. For example, given the 16analytes provided in Table 8 (A-P), a single color coding schemeencoding all 16 analytes may assign the values 1, 2, 4, 8, 16, 32, 64,128, 256, 512, 1024, 2048, 4096, 8192, and 16384 to analytes A, B, C, D,E, F, G, H, I, J, K, L, M, N, O, and P, respectively. Such a codingscheme is non-degenerate by design and the cumulative intensity resultcan be unambiguously decoded to indicate the presence or absence ofanalytes A-P. This coding scheme is capable of detecting the presence orabsence of M analytes, where M=log₂ (F+1) and F is the maximumcumulative value of a signal (e.g., signal intensity). By adding asecond component to this signal (e.g., color, as depicted in Table 8),the capacity of this coding scheme can be increased to M=C*log₂ (F+1),where C is the number of colors used in said coding scheme.

As described throughout this specification, any suitable value may beused for C or F. For example, C may be at least about 2, 3, 4, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,44, 45, 46, 47, 48, 49, 50, 60, 70, 80, 90, 100, or more. F may be atleast about 2, 4, 8, 16, 32, 64, 128, 255, 512, 1024, 2048, 4096, 8192,16384, 32768, 65536, 131072, 262144, 524288, 1048576, and so on. Asdescribed elsewhere in this disclosure, both the initial starting valueof F and the steps in its progression may also be varied.

III. Analytes

An analyte may be any suitable analyte that may be analyzed using themethods and compositions of the invention, where the analyte is capableof interacting with a reagent in order to generate a signal with atleast two components that can be measured. An analyte may benaturally-occurring or synthetic. An analyte may be present in a sampleobtained using any methods known in the art. In some cases, a sample maybe processed before analyzing it for an analyte. The methods andcompositions presented in this disclosure may be used in solution phaseassays, without the need for particles (such as beads) or a solidsupport.

In some cases, an analyte may be a polynucleotide, such as DNA, RNA,peptide nucleic acids, and any hybrid thereof, where the polynucleotidecontains any combination of deoxyribo- and/or ribo-nucleotides.Polynucleotides may be single stranded or double stranded, or containportions of both double stranded or single stranded sequence.Polynucleotides may contain any combination of nucleotides or bases,including, for example, uracil, adenine, thymine, cytosine, guanine,inosine, xanthine, hypoxanthine, isocytosine, isoguanine and anynucleotide derivative thereof. As used herein, the term “nucleotide” mayinclude nucleotides and nucleosides, as well as nucleoside andnucleotide analogs, and modified nucleotides, including both syntheticand naturally occurring species. Polynucleotides may be any suitablepolynucleotide for which one or more reagents (or probes) as describedherein may be produced, including but not limited to cDNA, mitochondrialDNA (mtDNA), messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA(tRNA), nuclear RNA (nRNA), small interfering RNA (siRNA), small nuclearRNA (snRNA), small nucleolar RNA (snoRNA), small Cajal body-specific RNA(scaRNA), microRNA (miRNA), double stranded (dsRNA), ribozyme,riboswitch or viral RNA. Polynucleotides may be contained within anysuitable vector, such as a plasmid, cosmid, fragment, chromosome, orgenome.

Genomic DNA may be obtained from naturally occurring or geneticallymodified organisms or from artificially or synthetically createdgenomes. Analytes comprising genomic DNA may be obtained from any sourceand using any methods known in the art. For example, genomic DNA may beisolated with or without amplification. Amplification may include PCRamplification, multiple displacement amplification (MDA), rolling circleamplification and other amplification methods. Genomic DNA may also beobtained by cloning or recombinant methods, such as those involvingplasmids and artificial chromosomes or other conventional methods (seeSambrook and Russell, Molecular Cloning: A Laboratory Manual., citedsupra.) Polynucleotides may be isolated using other methods known in theart, for example as disclosed in Genome Analysis: A Laboratory ManualSeries (Vols. I-IV) or Molecular Cloning: A Laboratory Manual. If theisolated polynucleotide is an mRNA, it may be reverse transcribed intocDNA using conventional techniques, as described in Sambrook andRussell, Molecular Cloning: A Laboratory Manual., cited supra.

An analyte may be a protein, polypeptide, lipid, carbohydrate, sugar,small molecule, or any other suitable molecule that can be detected withthe methods and compositions provided herein. An analyte may be anenzyme or other protein. An analyte may be a drug or metabolite (e.g.,anti-cancer drug, chemotherapeutic drug, anti-viral drug, antibioticdrug, or biologic). An analyte may be any molecule, such as a co-factor,receptor, receptor ligand, hormone, cytokine, blood factor, antigen,steroid, or antibody.

An analyte may be any molecule from any pathogen, such as a virus,bacteria, parasite, fungus, or prion (e.g., PrP^(Sc)). Examples ofviruses include those from the families Adenoviridae, Flaviviridae,Hepadnaviridae, Herpesviridae, Orthomyxoviridae, Papovaviridae,Paramyxoviridae, Picornaviridae, Polyomavirus, Retroviridae,Rhabdoviridae, and Togaviridae. Specific examples of viruses includeadenovirus, astrovirus, bocavirus, BK virus, coxsackievirus,cytomegalovirus, dengue virus, Ebola virus, enterovirus, Epstein-Barrvirus, feline leukemia virus, hepatitis virus, hepatitis A virus,hepatitis B virus, hepatitis C virus, hepatitis D virus, hepatitis Evirus, herpes simplex virus (HSV), HSV type 1, HSV type 2, humanimmunodeficiency virus (HIV), HIV type 1, HIV type 2, human papillomavirus (HPV), HPV type 1, HPV type 2, HPV type 3, HPV type 4, HPV type 6,HPV type 10, HPV type 11, HPV type 16, HPV type 18, HPV type 26, HPVtype 27, HPV type 28, HPV type 29, HPV type 30, HPV type 31, HPV type33, HPV type 34, HPV type 35, HPV type 39, HPV type 40, HPV type 41, HPVtype 42, HPV type 43, HPV type 44, HPV type 45, HPV type 49, HPV type51, HPV type 52, HPV type 54, HPV type 55, HPV type 56, HPV type 57, HPVtype 58, HPV type 59, HPV type 68, HPV type 69, influenza virus, JCvirus, Marburg virus, measles virus, mumps virus, Norwalk virus,parovirus, polio virus, rabies virus, respiratory syncytial virus,retrovirus, rhinovirus, rotavirus, Rubella virus, smallpox virus,vaccinia virus, West Nile virus, and yellow fever virus.

Examples of bacteria include those from the genuses Bordetella,Borrelia, Brucella, Campylobacter, Chlamydia, Clostridium,Corynebacterium, Enterococcus, Escherichia, Francisella, Haemophilus,Helicobacter, Legionella, Leptospira, Listeria, Mycobacterium,Mycoplasma, Neisseria, Pseudomonas, Rickettsia, Salmonella, Shigella,Staphylococcus, Streptococcus, Treponema, Vibrio, and Yersinia. Specificexamples of bacteria include Bordetella par apertussis, Bordetellapertussis, Borrelia burgdorferi, Brucella abortus, Brucella canis,Brucella melitensis, Brucella suis, Campylobacter jejuni, Chlamydiapneumoniae, Chlamydia psittaci, Chlamydia trachomatix, Clostridiumbotulinum, Clostridium difficile, Clostridium perfringens, Clostridiumtetani, Corynebacterium diphtherias, Enterococcus faecalis, Enterococcusfaecium, Escherichia coli, Francisella tularensis, Haemophilusinfluenzae, Helicobacter pylori, Legionella pneumophila, Leptospirainterrogans, Listeria monocytogenes, Mycobacterium leprae, Mycobacteriumtuberculosis, Mycobacterium ulcerans, Mycoplasma pneumoniae, Neisseriagonorrhoeae, Neisseria meningitidis, Pseudomonas aeruginosa, Rickettsiarickettsii, Salmonella choleraesuis, Salmonella dublin, Salmonellaenteritidis, Salmonella typhi, Salmonella typhimurium, Shigella sonnei,Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcussaprophyticus, Streptococcus agalactiae, Streptococcus pneumoniae,Streptococcus pyogenes, Treponema pallidum, Vibrio cholerae, Yersiniapestis, and Yersinia enterocolitica.

Examples of parasites include those from the genuses Acanthamoeba,Babesia, Balamuthia, Balantidium, Blasocystis, Cryptosporidium,Dientamoeba, Entamoeba, Giardia, Isospora, Leishmania, Naegleria,Pediculus, Plasmodium, Rhinosporidium, Sarcocystis, Schistosoma,Toxoplasma, Trichomonas, and Trypanosoma. Specific examples of parasitesinclude Babesia divergens, Babesia bigemina, Babesia equi, Babesiamicrofti, Babesia duncani, Balamuthia mandrillaris, Balantidium coli,Dientamoeba fragilis, Entamoeba histolytica, Giardia lamblia, Isosporabelli, Naegleria fowleri, Pediculus humanus, Plasmodium falciparum,Plasmodium knowlesi, Plasmodium malariae, Plasmodium ovale, Plasmodiumvivax, Rhinosporidium seeberi, Sarcocystis bovihominis, Sarcocystissuihominis, Schistosoma mansoni, Toxoplasma gondii, Trichomonasvaginalis, Trypanosoma brucei, and Trypansoma cruzi.

Examples of fungi include those from the genuses Apophysomyces,Aspergillus, Blastomyces, Candida, Cladosporium, Coddidioides,Cryptococcos, Exserohilum, Fusarium, Histoplasma, Pichia, Pneumocystis,Saccharomyces, Sporothrix, Stachybotrys, and Trichophyton. Specificexamples of fungi include Aspergillus fumigatus, Aspergillus flavus,Aspergillus clavatus, Blastomyces dermatitidis, Candida albicans,Coccidioides immitis, Crytptococcus neoformans, Exserohilum rostratum,Fusarium verticillioides, Histoplasma capsulatum, Pneumocystisjirovecii, Sporothrix schenckii, Stachybotrys chartarum, andTrichophyton mentagrophytes.

In some cases, the methods provided in this disclosure may be used todetect any one of the analytes described above, or elsewhere in thespecification. In some cases the methods provided in this disclosure maybe used to detect panels of the analytes described above, or elsewherein the specification. For example, a panel may comprise an analyteselected from the group consisting of any 2, 3, 4, 5, 6, 7, 8, 9, 10,11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28,29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46,47, 48, 49, 50, 60, 70, 80, 90, 100 or more analytes described above orelsewhere in the specification.

An analyte may be obtained from any suitable location, including fromorganisms, whole cells, cell preparations and cell-free compositionsfrom any organism, tissue, cell, or environment. Analytes may beobtained from environmental samples, biopsies, aspirates, formalin fixedembedded tissues, air, agricultural samples, soil samples, petroleumsamples, water samples, or dust samples. In some instances, an analytemay be obtained from bodily fluids which may include blood, urine,feces, serum, lymph, saliva, mucosal secretions, perspiration, centralnervous system fluid, vaginal fluid, or semen. Analytes may also beobtained from manufactured products, such as cosmetics, foods, personalcare products, and the like. Analytes may be the products ofexperimental manipulation including, recombinant cloning, polynucleotideamplification, polymerase chain reaction (PCR) amplification,purification methods (such as purification of genomic DNA or RNA), andsynthesis reactions.

More than one type of analyte may be detected in each multiplexed assay.For example, a polynucleotide, a protein, a polypeptide, a lipid, acarbohydrate, a sugar, a small molecule, or any other suitable moleculemay be detected simultaneously in the same multiplexed assay with theuse of suitable reagents. Any combination of analytes may be detected atthe same time.

Detection of an analyte may be useful for any suitable application,including research, clinical, diagnostic, prognostic, forensic, andmonitoring applications. Exemplary applications include detection ofhereditary diseases, identification of genetic fingerprints, diagnosisof infectious diseases, cloning of genes, paternity testing, criminalidentification, phylogeny, anti-bioterrorism, environmentalsurveillance, and DNA computing. For example, an analyte may beindicative of a disease or condition. An analyte may be used to make atreatment decision, or to assess the state of a disease. The presence ofan analyte may indicate an infection with a particular pathogen, or anyother disease, such as cancer, autoimmune disease, cardiorespiratorydisease, liver disease, digestive disease, and so on. The methodsprovided herein may thus be used to make a diagnosis and to make aclinical decision based on that diagnosis. For example, a result thatindicates the presence of a bacterial polynucleotide in a sample takenfrom a subject may lead to the treatment of the subject with anantibiotic.

In some cases the methods and compositions of the invention may be usedto detect at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55,60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170,180, 190, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1000analytes. In some cases the methods and compositions of the inventionmay be used to detect 7-50, 8-40, 9-30, 10-20, 10-15, 8-12, or 7-12analytes.

In some cases, this disclosure provides assays that are capable ofunambiguously detecting the presence or absence of each of 1, 2, 3, 4,5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41,42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95,100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 250, 300, 350,400, 450, 500, 600, 700, 800, 900, or 1000 analytes, in any combinationof presence or absence, in a single sample volume withoutimmobilization, separation, mass spectrometry, or melting curveanalysis. In some cases, this disclosure provides assays that arecapable of unambiguously detecting the presence or absence of each of atleast 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37,38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 60, 65, 70, 75,80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200,250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1000 analytes, inany combination of presence or absence, in a single sample volumewithout immobilization, separation, mass spectrometry, or melting curveanalysis. In some cases, this disclosure provides assays that arecapable of unambiguously detecting the presence or absence of less than1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38,39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 60, 65, 70, 75, 80,85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 250,300, 350, 400, 450, 500, 600, 700, 800, 900, or 1000 analytes, in anycombination of presence or absence, in a single sample volume withoutimmobilization, separation, mass spectrometry, or melting curveanalysis.

IV. Signals

The methods presented in this disclosure may be used with anyquantifiable signal. In some cases, this disclosure provides codingschemes and methods to encode an infinite number of targets withoutdegeneracy, using a single component of a signal (e.g., intensity). Forexample, as described above and in Example 3, a coding scheme may relyon a multiplicity of signal intensity without consideration of color.Although fluorescent probes have been used to illustrate this principle,the coding scheme is equally applicable to any other method providing aquantifiable signal, including an electrochemical signal and achemiluminescent signal, as described elsewhere in this disclosure.

The methods presented in this disclosure may also utilize themeasurement of a signal in at least two dimensions, also referred to asthe measurement of at least two components of a signal. In comparison tothe coding scheme described in the paragraph above, which relies on, forexample, signal intensity to differentiate between analytes, utilizationof at least two components of a signal (e.g., color and intensity)allows the generation of more unique codes per unit of signal intensitybandwidth. When at least two components of a signal are utilized, acumulative measurement of the at least two components may be obtainedfor a single sample volume. For example in the coding scheme describedin Table 5, the presence of each analyte results in a particularintensity (one component of the signal) in each of the four colors (asecond component of a signal). The combination of these constituentsignals leads to a cumulative signal that may be measured by measuringan intensity at each wavelength or range of wavelengths. Thecorresponding coding scheme or decoding matrix may then be used toconvert the cumulative measurement into a determination of the presenceor absence of an analyte.

In some cases, a quantifiable signal comprises a waveform that has botha frequency (wavelength) and an amplitude (intensity). A signal may bean electromagnetic signal. An electromagnetic signal may be a sound, aradio signal, a microwave signal, an infrared signal, a visible lightsignal, an ultraviolet light signal, an x-ray signal, or a gamma-raysignal. In some cases, an electromagnetic signal may be a fluorescentsignal, for example a fluorescence emission spectrum that may becharacterized in terms of wavelength and intensity.

In certain portions of this disclosure, the signal is described andexemplified in terms of a fluorescent signal. This is not meant to belimiting, and one of ordinary skill in the art will readily recognizethat the principles applicable to the measurement of a fluorescentsignal are also applicable to other signals. For example, likefluorescent signals, any of the electromagnetic signals described abovemay also be characterized in terms of a wavelength and an intensity. Thewavelength of a fluorescent signal may also be described in terms ofcolor. The color may be determined based on measuring intensity at aparticular wavelength or range of wavelengths, for example bydetermining a distribution of fluorescent intensity at differentwavelengths and/or by utilizing a band pass filter to determine thefluorescence intensity within a particular range of wavelengths. Suchband pass filters are commonly employed in a variety of laboratoryinstrumentation, including quantitative PCR machines. Intensity may bemeasured with a photodetector. A range of wavelengths may be referred toas a “channel.”

In some cases, the methods provided in this disclosure may be used withany signal where the cumulative signal scales with the constituentsignals of the same color, frequency, absorption band, and so on.However, the cumulative signal need not be digital or scale linearlywith the number and intensity of the constituent signals. For example,if the physical principle of measurement is absorption, the cumulativeattenuation is a product of constituent attenuations while theconstituent concentrations are additive, due to the exponential natureof the Beer-Lambert law. The logarithm of the cumulative attenuationwill then scale linearly with constituent concentrations in eachabsorption band (the equivalent of color, if fluorescent detection isused). The methods of the invention are therefore applicable. Themethods of the invention may also be used with chemiluminescent signalsand electrochemical signals.

The number of signals, and the number of dimensions or componentsmeasured, may also be expanded beyond the numbers shown in the exemplaryembodiments of the invention, leading to an expansion in multiplexingcapability. The exemplary embodiments provided in this disclosureutilize coding schemes constructed utilizing a fluorescent signal withone or two components measured: wavelength and/or intensity. The numberof analytes that can be encoded can be increased by increasing thenumber of wavelengths and/or intensities. The number of analytes thatcan be encoded can also be increased by increasing the number ofsignals, for example by combining a fluorescent signal with anelectrochemical signal or a FRET signal (fluorescence resonance energytransfer).

In some cases, more than two components of a signal may be measured. Forexample, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 18, 20or more components of a signal may be measured. At least 2, 3, 4, 5, 6,7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 18, or 20 components of asignal may be measured. At least 2, but fewer than 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 18, or 20 components of a signal maybe measured. In some cases, 2-3, 2-4, 2-5, 2-6, 3-5, 3-6, 3-8, or 5-10components of a signal may be measured. These additional components mayinclude kinetic components, such as a rate of signal decay and rate ofphotobleaching.

If a fluorescent signal is employed, the number of analytes that can beencoded may be further expanded by utilizing additional fluorophores.For example, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or morefluorophores may be used. In some cases, at least 1, 2, 3, 4, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,44, 45, 46, 47, 48, 49, or 50 fluorophores may be used. In some cases,fewer than 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36,37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 fluorophoresmay be used. In some cases, 4-6, 4-7, 4-8, 4-9, 4-10, 5-6, 5-7, 5-8,5-9, 5-10, 10-15, or 10-20 fluorophores may be used.

Generally, the number of analytes that can be encoded may be furtherexpanded by utilizing additional first values (e.g., intensities) thatare values or ranges of values from a first component of a signal. Forexample, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36,37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, or more firstvalues that are values or ranges of values from a first component of asignal may be used. In some cases, at least 1, 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45,46, 47, 48, 49, 50 or more first values that are values or ranges ofvalues from a first component of a signal may be used. In some cases,fewer than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 firstvalues that are values or ranges of values from a first component of asignal may be used. In some cases, 4-20, 4-6, 4-7, 4-8, 4-9, 4-10, 5-6,5-7, 5-8, 5-9, 5-10, 10-15, or 10-20 first values that are values orranges of values from a first component of a signal may be used.

In instances in which intensity is a component of a signal that isquantified, such as when a fluorescent signal is utilized, the presenceof an analyte may be encoded using a variety of intensities or ranges ofintensities. For example, a coding scheme may utilize 1, 2, 3, 4, 5, 6,7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,44, 45, 46, 47, 48, 49, 50, or more intensities or ranges ofintensities. A coding scheme may utilize at least 1, 2, 3, 4, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,44, 45, 46, 47, 48, 49, 50, or more intensities or ranges ofintensities. A coding scheme may utilize fewer than 2, 3, 4, 5, 6, 7, 8,9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26,27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44,45, 46, 47, 48, 49, or 50 intensities or ranges of intensities. In somecases, a coding scheme may utilize 2-20, 2-3, 2-4, 2-5, 2-6, 2-7, 2-8,2-9, 2-10, 3-4, 3-5, 3-6, 3-7, 3-8, 3-9, 3-10, 4-5, 4-6, 4-7, 4- 8, 4-9,4-10, 5-6, 5-7, 5-8, 5-9, or 5-10 intensities or ranges of intensities.

The number of analytes that can be encoded may be further expanded byutilizing additional second values (e.g., wavelengths) that are valuesor ranges of values from a second component of a signal. For example, 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39,40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, or more second values thatare values or ranges of values from a second component of a signal maybe used. In some cases, at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30,31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48,49, 50 or more second values that are values or ranges of values from asecond component of a signal may be used. In some cases, fewer than 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39,40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 second values that arevalues or ranges of values from a second component of a signal may beused. In some cases, 4-20, 4-6, 4-7, 4-8, 4-9, 4-10, 5-6, 5-7, 5-8, 5-9,5-10, 10-15, or 10-20 second values that are values or ranges of valuesfrom a second component of a signal may be used.

In instances in which wavelength is a component of a signal that isquantified, such as when a fluorescent signal is utilized, the presenceof an analyte may be encoded using a variety of wavelengths or ranges ofwavelengths. For example, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50,or more wavelengths or ranges of wavelengths may be used. In some cases,at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36,37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or morewavelengths or ranges of wavelengths may be used. In some cases, fewerthan 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37,38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 wavelengths orranges of wavelengths may be used. In some cases, 4-20, 4-6, 4-7, 4-8,4-9, 4-10, 5-6, 5-7, 5-8, 5-9, 5-10, 10-15, or 10-20 wavelengths orranges of wavelengths may be used.

In some cases, when degeneracy is eliminated, the methods of theinvention are capable of detecting the presence or absence of at least6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42,43, 44, 45, 46, 47, 48, 49, 50, or more analytes in a single volume wheneach reagent used to generate a signal in the volume generates only onesecond value (e.g., each reagent, emits light at only one wavelength).

In other cases, when degeneracy is eliminated, the methods of theinvention are capable of detecting the presence or absence of at least7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,44, 45, 46, 47, 48, 49, 50, or more analytes in a single volume using atotal of four second values in that volume (e.g., a total of fourwavelengths or ranges or wavelengths, which might be implemented byusing four spectrally resolvable fluorophores).

As described throughout the specification, the assay provided hereinutilizes cumulative measurements on a sample. A cumulative measurementmay be, for example, a single measurement of intensity values, or ameasurement of intensity values at one or more wavelengths or ranges ofwavelengths. A plurality of cumulative measurements may be obtained. Forexample, an intensity may be measured at 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28,29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46,47, 48, 49, 50, or more wavelengths or ranges of wavelengths. Anintensity may be measured at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29,30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50, or more wavelengths or ranges of wavelengths. An intensitymay be measured at less than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 wavelengths or ranges of wavelengths.

More generally a cumulative measurement may be obtained for anyquantifiable component of a signal, and for any quantifiable componentof a signal at another quantifiable component of a signal. For example,at least a first component of a signal may be measured at 1, 2, 3, 4, 5,6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42,43, 44, 45, 46, 47, 48, 49, 50, or more second components of a signal.At least a first component of a signal may be measured at at least 1, 2,3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40,41, 42, 43, 44, 45, 46, 47, 48, 49, 50, or more second components of asignal. At least a first component of a signal may be measured at lessthan 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37,38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 second componentsof a signal.

As is apparent from this disclosure, each analyte to be detected can beencoded as a code utilizing any number of suitable components of asignal or any number of signals. For example, each analyte to bedetected can be encoded in 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,50, or more components of a signal or signals. In some cases, eachanalyte to be detected can be encoded in at least 1, 2, 3, 4, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,44, 45, 46, 47, 48, 49, 50 or more components of a signal or signals. Insome cases, each analyte to be detected can be encoded in fewer than 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39,40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 components of a signal orsignals. In some cases, 1-4, 4-20, 4-6, 4-7, 4-8, 4-9, 4-10, 5-6, 5-7,5-8, 5-9, 5-10, 10-15, or 10-20 components of signal or signals may beused to encode each analyte. Each analyte in a coding scheme may beencoded by the same number of components of a signal, or signals, ordifferent numbers of components of a signal, or signals.

A. Probes, Primers, Fluorophores, and Quenchers

Some of the methods provided in this disclosure utilize a reagent thatgenerates a signal in the presence of an analyte. Any suitable reagentmay be used with the invention. Generally, a reagent will have ananalyte-specific component and a component that generates a signal inthe presence of the analyte. In some cases, these reagents are referredto as probes. The probes may be hybridization probes. The hybridizationprobes may be an oligonucleotide probe attached to a fluorophore and aquencher (e.g., a TAQMAN probe).

The methods of the invention may use one or more reagents or probes todetect the presence or absence of each analyte. For example, 1, 2, 3, 4,5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41,42, 43, 44, 45, 46, 47, 48, 49, 50 or more or probes may be used todetect the presence or absence of each analyte. In some cases, at least1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38,39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 probes may be used todetect the presence or absence of each analyte. In some cases, fewerthan 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38,39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 probes may be used todetect the presence or absence of each analyte. In some cases, thenumber of probes used to detect the presence or absence of each analyteis 1-10, 2-9, 2-8, 2-7, 2-6, 2-5, 2-4, 1-3, or 1-4.

In some cases, a sample is contacted with 4, 5, 6, 7, 8, 9, 10, 11, 12,13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30,31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48,49, 50, or more probes to detect the presence or absence of allanalytes. In some cases, a sample is contacted with at least 4, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,44, 45, 46, 47, 48, 49, 50 or more probes to detect the presence orabsence of all analytes. In some cases, a sample is contacted with fewerthan 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39,40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 probes to detect thepresence or absence of all analytes. In some cases, the number of probesthat a sample is contacted with to detect the presence or absence of allanalytes is 4-50, 4-40, 4-30, 4-20, 5-15, 5-10, or 3-10.

As described above, oligonucleotide probes attached to a fluorophore anda quencher may be used to detect the presence of an analyte in apolynucleotide amplification assay. So long as the quencher and thefluorophore are in proximity, the quencher quenches the fluorescenceemitted by the fluorophore upon excitation by a light source. Thesequence of the oligonucleotide probe is designed to be complementary toa polynucleotide sequence present in an analyte, and therefore capableof hybridizing to the polynucleotide sequence present in the analyte.Hybridization of the oligonucleotide probe may be performed in a nucleicacid amplification reaction comprising primers (e.g., a polymerase chainreaction). Upon extension of the primers by a DNA polymerase, the 5′ to3′ exonuclease activity of the polymerase degrades the probe, releasingthe fluorophore and the quencher into the medium. The proximity betweenthe fluorophore and the quencher is broken and the signal from thefluorophore is no longer quenched. Thus, the amount of fluorescencedetected is a function of the amount of analyte present. If no analyteis present, the probe will not hybridize to an analyte, and thefluorophore and quencher will remain in close proximity. Little or nosignal will be produced.

Oligonucleotide probes may have one or a plurality of fluorophores andquenchers per probe. For example, in some embodiments an oligonucleotideprobe may comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 ormore fluorophores. An oligonucleotide probe may comprise at least 1, 2,3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40,41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 fluorophores. Anoligonucleotide probe may comprise fewer than 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45,46, 47, 48, 49, or 50 fluorophores.

An oligonucleotide probe may comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29,30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50 or more quenchers. An oligonucleotide probe may comprise atleast 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37,38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 quenchers. Anoligonucleotide probe may comprise fewer than 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45,46, 47, 48, 49, or 50 quenchers.

Attachment of probes and quenchers to a probe may be performed in thesame reaction or in serial reactions. A series of reactions may beperformed to label probes with at least one fluorophore and the reactionproducts may be mixed to generate a mixture of probes with differentfluorophores.

If an oligonucleotide probe comprises two or more fluorophores, thesefluorophores may be arranged to allow Förster (Fluorescence) resonanceenergy transfer (FRET) to occur between the fluorophores. Briefly, FRETis a mechanism of energy transfer between fluorophores. Using FRET-basedprobes allows one excitation source to generate two differentfluorescence emission signals by excitation of a single fluorophore. Forexample, the methods described herein may used paired probes, where oneprobe in the pair is attached to a fluorophore and a quencher and asecond probe is attached to two fluorophores (in close enough proximityfor FRET to occur) and a quencher. Any combination of fluorophores andquenchers that provide for FRET may be used. Such an approach doublesthe number of fluorescent probes that may be used with an excitationsource, because a single excitation source can be used to produce twosignals: one from the probe with one fluorophore and one from the probewith two fluorophores in close enough proximity to provide for FRET. Forexample, using the encoding method described in Table 8, the number ofunambiguously detectable analytes could be increased from 16 to 32 bypairing each of the probes in Table 8 with a corresponding FRET probe.

The primers may be specific for a particular analyte and capable ofamplifying a region complementary to a probe. In some cases, the numberof pairs of primers used is equivalent to the number of probes. In othercases, the number of probes used may exceed the number of primer pairsused. In still other cases, the number of primer pairs used may exceedthe number of probes used. In some cases a sample to be analyzed iscontacted with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34,35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or morepairs of primers. In some cases a sample to be analyzed is contactedwith at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or more pairsof primers. In some cases a sample to be analyzed is contacted withfewer than 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36,37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 pairs ofprimers. In some cases, the number of pairs of primers is 2-10, 3-15,4-20, 3-10, 4-10, 5-10, 6-8, or 6-10.

The primers may amplify regions of a polynucleotide in which differentnumbers of hybridization probes hybridize. For example, at least onepair of primers may amplify a region complementary to at least 2, 3, 4,5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41,42, 43, 44, 45, 46, 47, 48, 49, or 50 hybridization probes. In somecases, all of said pairs of primers may amplify a region complementaryto at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36,37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 hybridizationprobes.

In one example, a first probe may be labeled with the fluorophore5′-fluorescein amidite (5′-FAM) and the quencher black hole quencher 1(BHQ-1). A second probe may be labeled with 5′-FAM in close proximity(e.g., attached to) to cyanine 5.5 (Cy5.5) and the quencher black holequencher 3 (BHQ-3). Upon digestion of the probe, via the nucleaseactivity of the polymerase, two fluorescent signals are generated from asingle excitation wavelength (e.g., 470 nm). The fluorophore from thefirst probe will fluoresce at about 520 nm. The fluorophores on thesecond probe undergo FRET. The donor fluorophore, FAM is excited by theexcitation light source (e.g., 470 nm) and transfers its energy to theacceptor fluorophore, Cy5.5. The acceptor fluorophore emits at about 705nm. These fluorophores and quenchers are merely exemplary. Anyfluorophores that can undergo FRET and any quenchers that can quenchfluorescence are suitable for use with the invention. Methods forproducing FRET-based probes are described in Jothikumar et al.,BioTechniques, 2009, 46(7):519-524.

In some examples, a single hybridization probe may be used for eachanalyte. In order to utilize multi-color encoding (e.g., as shown inTable 3), each probe may be labeled with a plurality of fluorophores atpre-determined ratios. The ratio may be determined so that a positivecontrol signal provides the same intensity as other positive controlsignals of the same intensity, in the same color. This approach reducesthe number of probes that must be synthesized and may be less expensiveto deploy than methods utilizing multiple probes. Moreover, in the caseof hybridization probes, it is easier to fit one hybridization probe toan analyte sequence than multiple probes.

Although many aspects of the invention are exemplified using nucleicacid-based probes, one of ordinary skill in the art will readilyrecognize that other forms of probes would work equally well with theinvention described in this disclosure. For example, a binding moleculespecific to an analyte could be used as a probe. Non-limiting exemplarybinding molecules include an antibody recognizing an analyte, andgenerating a signal in the presence of an analyte.

In embodiments of the invention that utilize fluorescent labels, anysuitable fluorescent label may be used. Exemplary fluorescent labelssuitable for use with the invention include rhodamine, rhodol,fluorescein, thiofluorescein, aminofluorescein, carboxyfluorescein,chlorofluorescein, methylfluorescein, sulfluorescein, aminorhodol,carboxyrhodol, chlororhodol, methylrhodol, sulforhodol; aminorhodamine,carboxyrhodamine, chlororhodamine, methylrhodamine, sulforhodamine, andthiorhodamine, cyanine, indocarbocyanine, oxacarbocyanine,thiacarbocyanine, merocyanine, cyanine 2, cyanine 3, cyanine 3.5,cyanine 5, cyanine 5.5, cyanine 7, oxadiazole derivatives,pyridyloxazole, nitrobenzoxadiazole, benzoxadiazole, pyrene derivatives,cascade blue, oxazine derivatives, Nile red, Nile blue, cresyl violet,oxazine 170, acridine derivatives, proflavin, acridine orange, acridineyellow, arylmethine derivatives, auramine, crystal violet, malachitegreen, tetrapyrrole derivatives, porphin, phtalocyanine, and bilirubin.Exemplary quenchers include black hole quenchers, such as BHQ-0, BHQ-1,BHQ-2, BHQ-3; ATTO quenchers, such as ATTO 540Q, ATTO580Q, and ATTO612Q;and the like.

The fluorophores that may be used with the invention are not limited toany of the fluorophores described herein. For example, fluorophores withimproved properties are continually developed, and these fluorophorescould readily be used with the methods provided in this disclosure. Suchimproved fluorophores include quantum dots, which may emit energy atdifferent wavelengths after being excited at a single wavelength. Theadvantage of using such fluorophores is that only a single excitationsource is needed, but many different signals may be quantified, forexample in terms of color and intensity. Moreover, fluorophores withnarrow emission spectra would be particularly useful with the methoddescribed herein, as such fluorophores could be included in multiplexassays with minimal or no overlap between their emission spectra,thereby offering many more “colors” and boosting significantly theoverall number of coded analytes.

In some cases, one or more reagents are lyophilized. Any suitablereagent may be lyophilized. For example, probes, primers, enzymes,antibodies, or any other reagent used for detection may be lyophilized.In some cases, a sample comprising an analyte may also be lyophilized.Lyophilization may be useful, for example, when distributing reagentsand/or samples in developing regions where access to cold storage isexpensive, not readily available, or not reliably available. In oneexample, lyophilized reagents comprise any probe or analyte-specificreagent described in this disclosure or otherwise suitable for use withthe invention. In another example, lyophilized reagents comprise PCRprimers. In yet another example, lyophilized reagents comprise reagentssuitable for performing a PCR reaction.

V. Analytical Techniques and Instrumentation

The methods provided herein are suitable for use with a variety ofdetection methods. For example, the methods may be applied using ananalytical technique that measures the wavelength and intensity of afluorescent signal. This may be accomplished by measuring the intensityof a signal across a spectrum of wavelengths, or by using band passfilters that restrict the passage of certain wavelengths of light,thereby allowing only light of certain wavelengths to reach aphotodetector. Many real-time PCR and quantitative PCR instrumentscomprise an excitation light source and band pass filters that enablethe detection of fluorescent signals in four colors (e.g., blue, green,yellow, and red). Therefore, the methods of the invention can be readilyapplied using instruments widely used in the art. Importantly, themethods and compositions provided herein may be used to detect multipleanalytes by obtaining a cumulative measurement on a single solution. Noseparation is necessary. The invention does not require the use of beadsor a solid phase. Of course, one of ordinary skill in the art wouldunderstand that the invention could be used with separation, beads, or asolid phase, if desired.

FIG. 5 shows two examples of instrumental configurations that may beused to obtain cumulative measurements useful for the methods of theinvention. With reference to FIG. 5 , an instrument with a detectorconfigured to detect both wavelength and intensity (e.g., a fluorometer)is shown in 501. With reference to 501, at least one excitation lightsource 502 is directed into a chamber 503 containing analytes andreagents that generate a signal in the presence of the analytes 504. Asdescribed elsewhere, the analyte may be a nucleic acid and the reagentsgenerating the signal may be hybridization probes comprising afluorophore and a quencher. If the analyte is present, an emissionsignal 505 is generated. In the configuration shown in 501, thewavelength and intensity of this emission signal are measured across aspectrum by a detector capable of generating a fluorescence emissionspectrum 506.

The wavelength and intensity may also be determined using a combinationof a photodetector and band pass filters. This configuration is used inseveral thermal cyclers known in the art. With reference to FIG. 5 , aninstrument with band pass filters and a photodetector is depicted in507. With reference to 507, at least one excitation light source 508 isdirected into a chamber 509 containing analytes and reagents thatgenerate a signal in the presence of the analytes 510. As describedelsewhere, the analyte may be a nucleic acid and the reagents generatingthe signal may be hybridization probes comprising a fluorophore and aquencher. If the analyte is present, an emission signal 511 isgenerated. In the configuration shown in 507, band pass filters 512,513, and 514 are used to restrict the passage of light to light withincertain ranges of wavelengths. For example band pass filter 512 mayrestrict the passage of light to light within wavelength range 1. Bandpass filter 513 may restrict the passage of light to light withinwavelength range 2. Band pass filter 514 may restrict the passage oflight to light within wavelength range 3. Any number of band passfilters (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or more) may beused with the invention. In addition, the positions of the band passfilters in 507 are not meant to be limiting. In some cases, emittedlight may be passed through more than one band pass filter at any time.In other cases, the band pass filters may be configured so that allemitted light passes through only one band pass filter at a time. Afterpassage through a band pass filter, filtered light 515, 516, and 517 isdetected by a photodetector. For example, filtered light 515 may belight within wavelength range 1, filtered light 516 may be light withinwavelength range 2, and filtered light 517 may be light withinwavelength range 3. The intensity of each of the filtered lights 515,516, and 517 may then be quantified by a photodetector 518.

The methods described in this disclosure are compatible with a varietyof amplification methods, including quantitative PCR (qPCR) methods, endpoint PCR methods, reverse transcriptase PCR, and digital PCR methods.Digital PCR methods (e.g., DROPLET DIGITAL (BIORAD) and DYNAMIC ARRAY(FLUIDIGM)) produce highly sensitive quantification of polynucleotidecopy numbers. The methods provided herein can be easily integrated intothese systems to significantly expand their throughput by allowingmultiplexing in a droplet or a dynamic array.

Similarly, the methods described in this disclosure may be applied in areal-time PCR assay. For example, real-time data may be fully recordedas the PCR runs to completion. The end-point values may then be decodedto indicate the presence or absence of analytes. The individual cyclethresholds (Ct) values may be analyzed for each color by detecting themaxima of the second derivative of the real-time curve in that color. Asa particular analyte is amplified, fluorophores are released from itscorresponding probes in the same ratios as the color multiplicities inthe coding of that sequence. Hence, e.g. a code of 1100 will have thesame Ct in blue and green, while a code of 1400 will have its green Ctprecede its blue Ct by 2 cycles. This additional data enablesdetermination of the identity and starting quantity of each analyte.

The methods described herein may also be used directly on a tissuesample. For example, a tissue sample may be obtained andphotolithographic methods may be used to build wells directly onto thetissue sample. The tissue sample may be fixed prior to building thewells. The tissue sample may then be analyzed by dispensing appropriatereagents into the wells in the tissue sample. The encoding and decodingmethods described in this disclosure may be used for the multiplexeddetection of analytes within the wells etched into the tissue. Each wellmay correspond to a single cell or a few cells, providing excellentspatial resolution when analyzing different portions of a tissue for ananalyte. This method may be used to detect analytes in different areasof the same tissue.

In some cases, instruments may be modified or constructed, for example,to provide additional excitation light sources, at multiple wavelength,and/or to provide additional band pass filters or a capability ofdetermining a complete spectrum. Including additional excitation sourceswould allow for the excitation of a larger variety of fluorophores.Including additional band pass filters, or modifying or constructing aninstrument capable of determining an entire spectrum allows detection ofa wider variety of emissions from fluorophores. These techniques can beused to increase the number of fluorophores that can be used with themethods described in this disclosure and, accordingly, to increase thenumber of analytes that be simultaneously detected.

In some cases, the methods described in this disclosure utilizeend-point PCR methods. However, in some cases a result may be obtainedbefore the end-point. This may be advantageous when, for example,results are needed as soon as possible. For example, in one casecalibration experiments are performed in which different startingconcentrations of an analyte are analyzed to determine the cycle numberat which the signal becomes saturated, as a function of the startingamount of the analyte. Using this data, a computer monitoring a PCRreaction in real-time can be programmed to search for saturation up tothe maximal cycle number according to the limit of detection (LOD) ofthe particular system. If there is no amplification of an analyte (e.g.,other than a positive control, if present), by the maximal cycle number,the result for that analyte is negative. If there is amplification ofthe analyte by the maximal cycle number, the result for that analyte ispositive and the saturation intensity in each color may be used todecode the result using the coding scheme. In both cases, there would beno need to run the PCR reaction beyond the number of cycles set by theLOD for that instrument. Although PCR has been used to illustrate thisquantitative method, one of ordinary skill in the art will readilyrecognize that similar principles could be applied in any catalyticsystem where the starting amount of an analyte limits the rate ofreaction, and the rate of reaction can be measured and reported by anevolution in a signal intensity over time.

VI. Compositions and Kits

This disclosure also provides compositions and kits for use with themethods described herein. The compositions may comprise any component,reaction mixture and/or intermediate described herein, as well as anycombination. For example, the disclosure provides detection reagents foruse with the methods provided herein. Any suitable detection reagentsmay be provided, including hybridization probes labeled with afluorophore and a quencher and primers, as described elsewhere in thespecification.

In some cases, compositions comprise reagents for the detection of atleast seven analytes using four fluorophores. In some cases,compositions comprise reagents for the detection of at least 5, 6, 7, 8,9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26,27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44,45, 46, 47, 48, 49, or 50 analytes using four fluorophores. In somecases, compositions comprise reagents for the detection of at least 6,7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,44, 45, 46, 47, 48, 49, or 50 analytes using five fluorophores. In somecases, compositions comprise reagents for the detection of at least 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,44, 45, 46, 47, 48, 49, or 50 analytes using six fluorophores. In somecases, compositions comprise reagents for the detection of at least 8,9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26,27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44,45, 46, 47, 48, 49, or 50 analytes using seven fluorophores.

In some cases the compositions comprise primers. The compositions maycomprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34,35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 pairsof primers.

The invention also provides kits for carrying out the methods of theinvention. Accordingly, a variety of kits are provided in suitablepackaging. The kits may be used for any one or more of the usesdescribed herein, and, accordingly, may contain instructions fordetecting the presence or absence of each analyte of a plurality ofanalytes. A kit may comprise a coding scheme, or a decoding matrix, toassist the user in converting a cumulative measurement to a resultindicating the presence or absence of each of a plurality of analytes. Akit may be a diagnostic kit, for example, a diagnostic kit suitable forthe detection of any analyte, including the analytes recited herein. Akit may contain any of the compositions provided in this disclosure,including those recited above.

FIG. 6 shows schematics of exemplary kits of the invention. Withreference to FIG. 6 , a kit comprising a kit body 601 is shown thatcontains reagents for the detection of analytes (e.g., polynucleotideprobes comprising a fluorophore and a quencher) 602 and primers for theamplification of a nucleic acid 603. The kit may also contain any otherreagents, such as reagents suitable for performing an amplificationreaction 604. In the embodiment depicted in 601, the reagents for thedetection of analytes and the primers are each contained in a singlevolume (e.g., tube or a bottle). However, these reagents may also beprovided in separate volumes, as depicted the kit body shown in 605. Thekit body 605 contains seven separate volumes. Three volumes (606, 607,and 608) contain reagents for the detection of analytes (or mixtures ofsuch reagents) and three volumes (609, 610, and 611) contain primers (ormixtures of primers). The kit may also contain reagents suitable forperforming an amplification reaction 604.

FIG. 6 is provided for illustrative purposes only. Any number ofreagents for the detection of analytes (e.g., probes) and any number ofprimers may be included in a single tube or bottle, as appropriate forthe application. For example, in some embodiments, 1, 2, 3, 4, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,44, 45, 46, 47, 48, 49, 50 or more reagents for the detection ofanalytes may be included in a single bottle. In other cases, 1, 2, 3, 4,5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41,42, 43, 44, 45, 46, 47, 48, 49, 50 or more primers for amplification maybe included in a single bottle or tube. In some cases, primers andprobes may be provided in the same bottle or tube. For example, 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40,41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or more probes may be providedper pair of primers. In other cases, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29,30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50 or more primers may be provided per pair of probes. The kitsmay contain 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or morebottles or tubes. Control analytes, and their associated detectionreagents and primers, may also be included in the kit. These may beincluded in a separate bottle or tube or, for example, included withinthe bottle or tube providing reagents for an amplification reaction 604.As described elsewhere in the specification, any reagent in the kits maybe lyophilized.

VII. Systems and Software

The methods of this disclosure may also be performed as part of asystem. For example, one or more steps of the methods described hereinmay be performed by software contained on a computer readable medium.The software may be used to encode analytes, check for degeneracy,reduce or eliminate degeneracy, and/or produce a decoding matrix. Thesoftware may also be used to convert cumulative measurements made on aninstrument (e.g., a PCR machine) into information concerning thepresence or absence of an analyte. For example, with reference to FIG. 4, a computer 401 may be connected to an input device 403, a display 402,and a printer 404. The computer may execute one or more of the steps ofany of the methods described in this disclosure, including, for example,encoding methods 410, analysis methods 420, and decoding methods 430. Acomputer may reduce or eliminate degeneracy, for example as part of theencoding methods 410. Similarly, a computer may generate a coding schemethat is non-degenerate by design using, for example, mathematicaliteration. A computer may also be connected to a network 405. Thenetwork may be a local network and/or the Internet. The network may beused to perform the methods of the invention on multiple computers indifferent locations. For example, one computer may perform the encoding,another computer may perform the measuring, and yet another computer mayperform the decoding. A computer may perform any or all of thesemethods. The network may be used to transmit information obtained usingthe methods described in this disclosure throughout the world, forexample across a border.

In one example, the software is embedded in the instrument making themeasurement, such as a thermal cycler. In another example, the softwareis installed on a computer attached to the instrument making themeasurement, such as a computer attached to a thermal cycler. In anotherexample, the software is in the “cloud”—i.e., on a computer that anothercomputer may communicate with through a network.

Each of the elements described above may be connected to a controllerthat communicates with each of the elements and coordinates theiractions. For example, a controller may initiate the encoding of a seriesof analytes into values of color and intensity. As described throughoutthis disclosure, the controller can execute software to reduce oreliminate degeneracy by removing one or more potential analyte codesfrom the encoding matrix. The controller may then automatically orderprobes corresponding to this code from a manufacturer of probes.Alternatively, the controller may operate an oligonucleotide synthesisinstrument that can synthesize the appropriate probes. After analysis ofthe sample on the instrument (which may also be automated), thecontroller may process the results of the analysis using the decodingmatrix. The controller may then provide these results to a user.

VIII. Services

The methods provided herein may also be performed as a service. Forexample, a service provider may obtain the identity of a plurality ofanalytes that a customer wishes to analyze. The service provider maythen encode each analyte to be detected by any of the methods describedherein and provide appropriate reagents to the customer for the assay.The customer may perform the assay and provide the results to theservice provider for decoding. The service provider may then provide thedecoded results to the customer. The customer may also encode analytes,generate probes, and/or decode results by interacting with softwareinstalled locally (at the customer's location) or remotely (e.g., on aserver reachable through a network). Exemplary customers includeclinical laboratories, physicians, manufacturers of food and consumerproducts, industrial manufacturers (e.g., petroleum companies) and thelike. A customer or party may be any suitable customer or party with aneed or desire to use the methods, systems, compositions, and kits ofthe invention.

EXAMPLES Example 1: General Materials & Methods

1. General Reagents

TE Buffer, pH7 (LIFE TECHNOLOGIES, Carlsbad, CA); UltraPure RNAse-freeWater (LIFE TECHNOLOGIES, Carlsbad, CA); Taq 5× Master Mix (FISHERSCIENTIFIC COMPANY, Tustin, CA).

2. DNA Sequences, Primers, and Probes

Five nucleic acids from organisms of clinical relevance were chosen forthe exemplary study: (1) human immunodeficiency virus 1 (HIV-1); (2)Plasmodium falciparum (Malaria); (3) herpes simplex virus-2 (HSV-2); (4)Mycobacterium tuberculosis (TB); (5) and dengue virus type 3 (denguefever).

Two regions of diagnostic relevance from the HIV-1 genome, p17 andpoly-protease, were selected from the Los Alamos National LaboratoryHIV-1 reference sequence. A diagnostic sequence from the Plasmodiumfalciparum ChR7 gene was obtained from the UCSC Plasmodium falciparumGenome Browser. A sequence for Herpes Simplex Virus-2 was synthesizedfrom the sequence obtained from the European Molecular Biology Library.Similarly a diagnostic sequence for the rpoB gene in Mycobacteriumtuberculosis was synthesized from a sequence obtained from the EuropeanMolecular Biology Library. A PCR diagnostic sequence for Dengue VirusType 3 was obtained from the National Institute of Health geneticsequence database.

Oligonucleotides were synthesized by INTEGRATED DNA TECHNOLOGIES (IDT).Probes and primer pairs were chosen for each analyte usingOLIGOANALYZER, from IDT. Sense probes containing a fluorophore at the 5′end and a quencher at the 3′ end were synthesized for all analytes. Alloligonucleotides were lyophilized and reconstituted in TE buffer beforeuse. Tables 9-14 show sequence information, target sequence, primers,and probes for each of the six analytes.

TABLE 9 HIV-1 polyprotease sequence information. Sequence HIV-1 Poly protease 198mer synthesized   Informationfrom bases 2253-2550 Source HIV-1 Reference Sequence, Los Alamos  National Laboratory Target  GGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATsequence  TAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAA (3′ to 5′)ATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAAC ATAATTGG (SEQ ID NO: 1) Forward GGAAGCTCTATTAGATACAGGAGCAG  Primer  (SEQ ID NO: 2) (3′ to 5′) Reverse CCAATTATGTTGACAGGTGTAGGTCC  Primer  (SEQ ID NO: 3) (3′ to 5′) Probe 1 /56-FAM/TGAGTTTGCCAGGAAGATGGAAACCA/  (3′ to 5′) 3BHQ_1/ (SEQ ID NO: 4)

TABLE 10 HIV p17 sequence information. Sequence HIV-1 P17 199mer synthesized from bases  Name 790-1186 SourceHIV-1 Reference Sequence, Los Alamos  National Laboratory Target CAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTA sequence GATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCA (3′ to 5′)TCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCA   (SEQ ID NO: 5) Forward CAGCTACAACCATCCCTTCAGACA (SEQ ID NO: 6)   Primer  (3′ to 5′) Reverse TGACCTGATTGCTGTGTCCTGTGT (SEQ ID NO: 7) Primer  (3′ to 5′) Probe 1 /56-FAM/AGCAACCCTCTATTGTGTGCATCAAAGG/  (3′ to 5′) 3BHQ_1 (SEQ ID NO: 8)Probe 2  /5Cy3/AAAGCACAGCAAGCAGCAGCTGA/3BHQ_2/  (3′ to 5′)(SEQ ID NO: 9)

TABLE 11 Plasmodium ChR7 sequence information. Sequence Plasmodium ChR7 199mer synthesized from  Name bases 1139138-1141223Source UCSC Plasmodium falciparum Genome  Browser Gateway Target GCCTAACATGGCTATGACGGGTAACGGGGAATTAGAGTTC sequence GATTCCGGAGAGGGAGCCTGAGAAATAGCTACCACATCTA (3′ to 5′)AGGAAGGCAGCAGGCGCGTAAATTACCCAATTCTAAAGAAGAGAGGTAGTGACAAGAAATAACAATGCAAGGCCAATTTAAAACCTTCCCAGAGTAACAATTGGAGGGCAAGTCTGGTG  (SEQ ID NO: 10) Forward GCCTAACATGGCTATGACGGGTAA (SEQ ID NO: 11) Primer  (3′ to 5′) Reverse CACCAGACTTGCCCTCCAATTGTT (SEQ ID NO: 12) Primer  (3′ to 5′) Probe 1/56-FAM/ATTCCGGAGAGGGAGCCTGAGAAATA/  (3′ to 5′) 3BHQ_1/ (SEQ ID NO: 13)Probe 2 /56-ROXN/AAGGAAGGCAGCAGGCGCGTAAATTA/  (3′ to 5′)3BHQ_2/ (SEQ ID NO: 14)

TABLE 12 Herpes simplex virus 2 sequence information. Sequence HSV-2 193mer synthesized from HSV-2  Name genome SourceEMBL Bank AJ303204 Target  TCAGCCCATCCTCCTTCGGCAGTATGGAGGGTGTCGCGGCsequence  GGCGAGCCGCCGTCCCCAAAGACGTGCGGGTCGTACACGT (3′ to 5′)ACACGTACCAGGGCGGCGGGCCTCCGACCCGGTACGCTCTCGTAAATGCTTCCCTGCTGGTGCCGATCTGGGACCGCGCCGCGGAGACATTCGAGTACCAGATCGAACTCGG (SEQ  ID NO: 15) Forward  TCAGCCCATCCTCCTTCGGCAGTAT (SEQ ID NO: 16) Primer  (3′ to 5′) Reverse  CCGAGTTCGATCTGGTACTCGAATGT (SEQ ID NO:  Primer  17) (3′ to 5′) Probe 1 /56-FAM/AAAGACGTGCGGGTCGTACACGTACA/  (3′ to 5′) 3BHQ_1/ (SEQ ID NO: 18)Probe 2  /5Cy5/TAAATGCTTCCCTGCTGGTGCCGAT/  (3′ to 5′)3IAbRQSp/ (SEQ ID NO: 19)

TABLE 13 Mycobacterium tuberculosis rpoB sequence  information Sequence Mycobacterium Tuberculosis rpoB 200mer   Namesynthesized from Mycobacterium   tuberculosis rpoB genome SourceEMBL Bank GQ395623 Target  GAGTGCAAAGACAAGGACATGACGTACGCGGCCCCGCTGTsequence  TCGTCACGGCCGAGTTCATCAACAACAACACCGGCGAGAT (3′ to 5′)CAAGAGCCAGACGGTGTTCATGGGTGACTTCCCGATGATGACCGAGAAGGGCACCTTCATCATCAACGGCACCGAGCGCGTCGTGGTCAGCCAGCTGGTCCGCTCGCCCGGTGTGTACTT  (SEQ ID NO: 20) Forward  GAGTGCAAAGACAAGGACATGACG (SEQ ID NO: 21) Primer  (3′ to 5′) Reverse  AAGTACACACCGGGCGAGC (SEQ ID NO: 22) Primer  (3′ to 5′) Probe 1 /56-FAM/CGCTGTTCGTCACGGCCGAGTTCAT/3  (3′ to 5′) BHQ_1/ (SEQ ID NO: 23)Probe 2  /5Cy3/AGATCAAGAGCCAGACGGTGTTCATG/  (3′ to 5′)3BHQ_2/ (SEQ ID NO: 24) Probe 3  /5Cy5/AAGGGCACCTTCATCATCAACGGCA/ (3′ to 5′) 3IAbRQSp/ (SEQ ID NO: 25)

TABLE 14 Dengue virus type 3 sequence information. Sequence Dengue Virus Type 3 200mer synthesized    Namefrom Dengue Virus Type 3 genome Source GenBank M93130 Target ATGCCAACTGTGATTGAGCACTTAGAAAGACTACAAAGGA sequence AACATGGAGGAATGCTTGTGAGAAATCCACTCTCACGAAA (3′ to 5′)CTCCACGCACGAAATGTATTGGATATCCAATGGTACAGGCAACATCGTCTCATTCACAATGACACACAGGAGACCCACCATAGAGAAAGATGTGGATTTAGGAGCAGGAACCCGACATGT  (SEQ ID NO: 26) Forward ATGCCAACTGTGATTGAGCACT (SEQ ID NO: 27) Primer  (3′ to 5′) Reverse ACATGTCGGGTTCCTGCTCCTAAA (SEQ ID NO: 28) Primer  (3′ to 5′) Probe 1 /56-FAM/ACAAAGGAAACATGGAGGAATGCTTGTGA/  (3′ to 5′)3BHQ_1/ (SEQ ID NO: 29) Probe 2 /5Cy3/ACTCTCACGAAACTCCACGCACGAAA/3BHQ_2/  (3′ to 5′) (SEQ ID NO: 30)Probe 3  /56-ROXN/ACAATGACACACAGGAGACCCACCAT/ (3′ to 5′)3BHQ_2/ (SEQ ID NO: 31) Probe 4  /5Cy5/GGATATCCAATGGTACAGGCAACATCGT/ (3′ to 5′) 3IAbRQSp/ (SEQ ID NO: 32)3. Polymerase Chain Reactions

All PCR reactions were performed in a ROCHE 480 LIGHTCYCLER instrument.Forty-five thermal cycles were performed, with a 60 second hot-start at95° C. The cycling conditions for denaturation, annealing, and extensionwere 45 seconds, 50 seconds, and 60 seconds at 95° C., 65° C., and 70°C., respectively. Each experiment was run in quintuplicate, with areaction volume of 15 μL. Fluorescence measurements were obtained in thefollowing channels after every annealing step: 483 nm to 533 nm (FAM),523 nm to 568 nm (Cy3), 558 nm to 610 nm (ROX), and 615 nm to 670 nm(Cy5). Fluorescence measurements were also obtained after the hot-startand the end of the 45 thermal cycles. The change in the fluorescenceintensity between these two measurements (after hot-start and at the endof the 45 cycles) determined the end-point fluorescent signal.

Example 2: Simultaneous Detection of Polynucleotide Markers fromPathogens Based on an Encoding Method Using More Than One Color PerAnalyte

This example describes the simultaneous detection of up to fourpolynucleotides selected from HIV (2 polynucleotides), HSV-2,Mycobacterium, Plasmodium, and dengue virus. Fourteen PCR reactions wereassembled, using the reagents described in Table 15.

TABLE 15 Reagents for 14 PCR reactions. Reaction Type of No. ReagentReagent Concentration Volume 1 UltraPure Water — 34 μL Taq 5x Master Mix— 42 μL Template Poly Protease Template 17 nM 2 μL Primers Poly ProteaseFWD Primer 1 nM 2 μL Protease RVS Primer 1 nM 2 μL Probe Poly ProteaseProbe 1 1 nM 2 μL 2 UltraPure Water — 28 μL Taq 5x Master Mix — 42 μLTemplates Malaria Template 15 nM 2 μL Herpes Template 17 nM 2 μL TBTemplate 16 nM 2 μL Dengue Virus Template 17 nM 2 μL Primers PolyProtease FWD Primer 1 nM 2 μL Protease RVS Primer 1 nM 2 μL Probe PolyProtease Probe 1 1 nM 2 μL 3 UltraPure Water — 32 μL Taq 5x Master Mix —42 μL Template Malaria Template 15 nM 2 μL Primers Malaria FWD Primer 1μM 2 μL Malaria RVS Primer 1 μM 2 μL Probes Malaria Probe 1 1 μM 2 μLMalaria Probe 2 1 μM 2 μL 4 UltraPure Water — 26 μL Taq 5x Master Mix —42 μL Templates Poly Protease Template 17 nM 2 μL Herpes Template 17 nM2 μL TB Template 16 nM 2 μL Dengue Virus Template 17 nM 2 μL PrimersMalaria FWD Primer 1 μM 2 μL Malaria RVS Primer 1 μM 2 μL Probes MalariaProbe 1 1 μM 2 μL Malaria Probe 2 1 μM 2 μL 5 UltraPure Water — 32 μLTaq 5x Master Mix — 42 μL Template Herpes Template 17 nM 2 μL PrimersHerpes FWD Primer 1 μM 2 μL Herpes RVS Primer 1 μM 2 μL Probes HerpesProbe 1 1 μM 2 μL Herpes Probe 2 1 μM 2 μL 6 UltraPure Water — 26 μL Taq5x Master Mix — 42 μL Templates Poly Protease Template 17 nM 2 μLMalaria Template 15 nM 2 μL TB Template 16 nM 2 μL Dengue Virus Template17 nM 2 μL Primers Herpes FWD Primer 1 μM 2 μL Herpes RVS Primer 1 μM 2μL Probes Herpes Probe 1 1 μM 2 μL Herpes Probe 2 1 μM 2 μL 7 UltraPureWater — 30 μL Taq 5x Master Mix — 42 μL Template TB Template 16 nM 2 μLPrimers TB FWD Primer 1 μM 2 μL TB RVS Primer 1 μM 2 μL Probes TB Probe1 1 μM 2 μL TB Probe 2 1 μM 2 μL TB Probe 3 1 μM 2 μL 8 UltraPure Water— 30 μL Taq 5x Master Mix — 42 μL Templates Poly Protease Template 17 nM2 μL Malaria Template 15 nM 2 μL Herpes Template 17 nM 2 μL Dengue VirusTemplate 17 nM 2 μL Primers TB FWD Primer 1 μM 2 μL TB RVS Primer 1 μM 2μL Probes TB Probe 1 1 μM 2 μL TB Probe 2 1 μM 2 μL TB Probe 3 1 μM 2 μL9 UltraPure Water — 28 μL Taq 5x Master Mix — 42 μL Template DengueVirus Template 17 nM 2 μL Primers Dengue Virus FWD Primer 1 μM 2 μLDengue Virus RVS Primer 1 μM 2 μL Probes Dengue Virus Probe 1 1 μM 2 μLDengueVirus Probe 2 1 μM 2 μL Dengue Virus Probe 3 1 μM 2 μL DengueVirus Probe 4 1 μM 2 μL 10 UltraPure Water — 22 μL Taq 5x Master Mix —42 μL Templates Poly Protease Template 17 nM 2 μL Malaria Template 15 nM2 μL Herpes Template 17 nM 2 μL TB Template 16 nM 2 μL Primers DengueVirus FWD Primer 1 μM 2 μL Dengue Virus RVS Primer 1 μM 2 μL ProbesDengue Virus Probe 1 1 μM 2 μL Dengue Virus Probe 2 1 μM 2 μL DengueVirus Probe 3 1 μM 2 μL Dengue Virus Probe 4 1 μM 2 μL 11 Taq 5x MasterMix — 42 μL Templates Poly Protease Template 17 nM 2 μL Malaria Template15 nM 2 μL Herpes Template 17 nM 2 μL Dengue Virus Template 17 nM 2 μLPrimers Poly Protease FWD Primer 1 μM 2 μL Poly Protease RVS Primer 1 μM2 μL Malaria FWD Primer 1 μM 2 μL Malaria RVS Primer 1 μM 2 μL HerpesFWD Primer 1 μM 2 μL Herpes RVS Primer 1 μM 2 μL Dengue Virus FWD Primer1 μM 2 μL Dengue Virus RVS Primer 1 μM 2 μL Probes Poly Protease Probe 11 μM 2 μL Malaria Probe 1 1 μM 2 μL Malaria Probe 2 1 μM 2 μL HerpesProbe 1 1 μM 2 μL Herpes Probe 2 1 μM 2 μL Dengue Virus Probe 1 1 μM 2μL Dengue Virus Probe 2 1 μM 2 μL Dengue Virus Probe 3 1 μM 2 μL DengueVirus Probe 4 1 μM 2 μL 12 UltraPure Water — 2 μL Taq 5x Master Mix — 42μL Templates Poly Protease Template 17 nM 2 μL Malaria Template 15 nM 2μL Herpes Template 17 nM 2 μL TB Template 16 nM 2 μL Primers PolyProtease FWD Primer 1 μM 2 μL Poly Protease FWD Primer 1 μM 2 μL MalariaFWD Primer 1 μM 2 μL Malaria RVS Primer 1 μM 2 μL Herpes FWD Primer 1 μM2 μL Herpes RVS Primer 1 μM 2 μL TB FWD Primer 1 μM 2 μL TB RVS Primer 1μM 2 μL Probes Poly Protease Probe 1 1 μM 2 μL Malaria Probe 1 1 μM 2 μLMalaria Probe 2 1 μM 2 μL Herpes Probe 1 1 μM 2 μL Herpes Probe 2 1 μM 2μL TB Probe 1 1 μM 2 μL TB Probe 2 1 μM 2 μL TB Probe 3 1 μM 2 μL 13UltraPure Water — 12 μL Taq 5x Master Mix — 42 μL Templates PolyProtease Template 17 nM 2 μL Herpes Template 17 nM 2 μL TB Template 16nM 2 μL Primers Poly Protease FWD Primer 1 μM 2 μL Poly Protease FWDPrimer 1 μM 2 μL Herpes FWD Primer 1 μM 2 μL Herpes RVS Primer 1 μM 2 μLTB FWD Primer 1 μM 2 μL TB RVS Primer 1 μM 2 μL Probes Poly ProteaseProbe 1 1 μM 2 μL Herpes Probe 1 1 μM 2 μL Herpes Probe 2 1 μM 2 μL TBProbe 1 1 μM 2 μL TB Probe 2 1 μM 2 μL TB Probe 3 1 μM 2 μL 14 UltraPureWater — 10 μL Taq 5x Master Mix — 42 μL Templates Poly Protease Template17 nM 2 μL Malaria Template 15 nM 2 μL Dengue Virus Template 17 nM 2 μLPrimers Poly Protease FWD Primer 1 μM 2 μL Poly Protease FWD Primer 1 μM2 μL Malaria FWD Primer 1 μM 2 μL Malaria RVS Primer 1 μM 2 μL DengueVirus FWD Primer 1 μM 2 μL Dengue Virus RVS Primer 1 μM 2 μL Probes PolyProtease Probe 1 1 μM 2 μL Malaria Probe 1 1 μM 2 μL Malaria Probe 2 1μM 2 μL Dengue Virus Probe 1 1 μM 2 μL Dengue Virus Probe 2 1 μM 2 μLDengue Virus Probe 3 1 μM 2 μL Dengue Virus Probe 4 1 μM 2 μL

Referring to Table 15, reactions 1, 3, 5, 7, and 9 (containing HIVpolyprotease, Plasmodium, HSV, Mycobacterium, and dengue analytes,respectively) were positive controls that provided baseline fluorescenceintensity for each polynucleotide analytes alone, in the absence ofother analytes. The change in fluorescence intensity in each color wasused to provide the expected cumulative intensity level for each colorin the chromatogram (FIG. 3 ), as described more fully below. Reactions2, 4, 6, 8, and 10 were negative controls used to determine the extentof non-specific amplification. In these reactions, the primers providedwere not specific for the analytes provided.

Experiments 11, 12, 13, and 14 were multiplex detection experiments.Encoding was performed as indicated in Table 16. The measuredfluorescence intensity for each assay, in each color, was plotted asblack circles in the chromatogram of FIG. 3 .

TABLE 16 Coding scheme for detection of pathogens. FAM Cy3 ROX Cy5 HIVpoly-protease 1 0 0 0 HIV p17 1 1 0 0 Plasmodium 1 0 1 0 HSV 1 0 0 1Mycobacterium 1 1 0 1 Dengue Virus 1 1 1 1

To construct the chromatogram, the signals of the positive controls(reactions 1, 3, 5, 7, and 9) were used to assemble every possiblecombination of present sequences, in each color. The cumulative signalswere plotted in a diagram, called a “chromatogram” (FIG. 3 ). Cumulativesignals corresponding to all possible combinations of the same rank inthe same color were organized into their own “band.” Doing this for allfour colors produced a level and band structure, against which theexperimental results of each combination (reactions 11, 12, 13, and 14)could be evaluated. FIG. 3 shows three replicates of a chromatogramconstructed using the positive control samples, with experimentalresults 4112, 3121, and 3102 superimposed on the chromatogram. Theexperimental results are indicated by black dots.

The intensity value for each color in reactions 11-14 was measure inarbitrary fluorescence units (AFU), plotted on the chromatogram, andthen assigned to a band based on two criteria. First, if an experimentalresult was within a band, then the result was assigned to themultiplicity of the band (e.g., the Cy3 value of 1 in the left-mostchromatogram of FIG. 3 ). Second, if an experimental result was betweentwo bands, a two-step analysis was employed. If the experimental resultwas between two legitimate results, the experimental result was assignedto the closest band. (e.g., the Cy5 value of 2 in the right-mostchromatogram of FIG. 3 ). If the experimental result was between alegitimate result and an illegitimate result, the result was assigned tothe band with the legitimate result (e.g., the FAM value of 3 in themiddle chromatogram of FIG. 3 ). FIG. 8 schematically shows a legitimateresult of 4112 (top) indicating the presence of HIV polyprotease,Plasmodium, herpes simplex, and Mycobacterium; and an illegitimateresult of 4110 (bottom), which cannot be decoded and indicates amalfunction in the assay.

Using these criteria, the output of Experiment 12 was designated 4112,which was the correct answer. The output of Experiment 14 could havebeen designated as 2121 or 3121, but 2121 is illegitimate, so the resultmust be 3121, which is the correct answer. The output of Experiment 13could be designated as 3102 or 3101, both of which are legitimate, butthe result is clearly closer to 2 than 1 in the Cy5 channel, so 3102,the correct answer, was designated as the result. These results provideexperimental validation of the methods of the provided herein.

The results indicate a trend of slightly lower combined signal than whatwould be expected from a simple summation of positive-control signals.This may be because the combination of signals is not perfectly linear.This may be a result of additional effects for which the chromatogramconstruction does not account for at present. These effects may berelated to the absolute concentration of quenchers. The higher theabsolute concentration of quenchers, the larger the percentage ofreaction volume they quench, so that the same percentage of releasedfluorophores fails to contribute as much as expected to the cumulativesignal. One solution to this problem is to use low concentrations ofprobes, so that the percentile loss in signal is negligible, regardlessof how much quencher is released.

FIG. 3 shows that each rank containing multiple combinations has arelatively wide band. The width of the band is ultimately the differencebetween the highest and lowest cumulative signals for the positivecontrol samples. If all positive controls in the particular colorproduced exactly the same fluorescence signal, then the width of eachband would be zero. Since instead those signals are somewhat different,the resulting bands are relatively wide. However, there is a simplemeans to tighten the bands. Instead of loading all probes at the sameconcentration, as was done for the experiment above, the concentrationof each probe can be adjusted so that each of the resultingpositive-control signals is the same as the others in the same color.This approach would significantly tighten the bands, making it easier todetermine the multiplicity of a signal for a sample containing analytes.

Example 3: Simultaneous Detection of Polynucleotide Markers fromPathogens Based on an Encoding Method Using One Color Per Analyte andDifferent Intensities

This example describes the simultaneous detection of up to threepolynucleotides selected from dengue virus, HIV p17, and HIVpolyprotease. The coding scheme was as depicted in Table 11. As shown inTable 17, each analyte was encoded as a single value of fluorescenceintensity in a single color. In this case, as described elsewhere inthis disclosure, the coding scheme is non-degenerate by design. This isachieved by assigning an intensity value to each analyte that is equalto the cumulative intensity values for the prior analytes, plus one. Ofcourse, as described elsewhere in the specification, the initialassigned value can be greater than one, for example to betterdistinguish over noise. Similarly, the values assigned to each analytecan be greater than the cumulative intensity values for the prioranalytes plus one, for example, to increase the separation between theintensities and enable more simple assignment of intensities.

TABLE 17 Coding scheme for detection of dengue virus, HIV polyprotease,and HIV p17. FAM Dengue Virus 1 HIV p17 2 HIV polyprotease 4

The same reagents (e.g., templates, primers, and probes) used in Example2 were used here. The fluorescence signals generated by the respectiveprobes in positive-control end-point PCR reactions were measured andused to calculate the probe concentrations that would produce 1×, 2×,and 4× signal intensities. Experiments were then set up to detect theseven non-null combinations of analyte occurrences. Tables 18-24 providethe PCR reaction components for each of these mixtures.

TABLE 18 Binary FAM Experiment 1 Cocktail: HIV polyprotease, HIV p17,and dengue virus Concentration Volume Added Reagents UltraPure Water —50 μL Taq 5x Master Mix — 25 μL Templates Poly Protease Template 17 nM 4μL P17 Template 15 nM 4 μL Dengue Virus Template 17 nM 4 μL Primers PolyProtease FWD Primer 1 μM 4 μL Poly Protease RVS Primer 1 μM 4 μL P17 FWDPrimer 1 μM 4 μL P17 RVS Primer 1 μM 4 μL Dengue Virus FWD Primer 1 μM 4μL Dengue Virus RVS Primer 1 μM 4 μL Probes Poly Protease Probe 1 800 nM4 μL P17 Probe 1 400 nM 4 μL Dengue Virus Probe 1 200 nM 4 μL

TABLE 19 Binary FAM Experiment 2 Cocktail: dengue virus and HIV p17Concentration Volume Added Reagents UltraPure Water — 54 μL Taq 5xMaster Mix — 25 μL Templates Poly Protease Template 17 nM — P17 Template15 nM 4 μL Dengue Virus Template 17 nM 4 μL Primers Poly Protease FWDPrimer 1 μM 4 μL Poly Protease RVS Primer 1 μM 4 μL P17 FWD Primer 1 μM4 μL P17 RVS Primer 1 μM 4 μL Dengue Virus FWD Primer 1 μM 4 μL DengueVirus RVS Primer 1 μM 4 μL Probes Poly Protease Probe 1 800 nM 4 μL P17Probe 1 400 nM 4 μL Dengue Virus Probe 1 200 nM 4 μL

TABLE 20 Binary FAM Experiment 3 Cocktail: dengue virus and HIVpolyprotease Concentration Volume Added Reagents UltraPure Water — 54 μLTaq 5x Master Mix — 25 μL Templates Poly Protease Template 17 nM 4 μLP17 Template 15 nM — Dengue Virus Template 17 nM 4 μL Primers PolyProtease FWD Primer 1 μM 4 μL Poly Protease RVS Primer 1 μM 4 μL P17 FWDPrimer 1 μM 4 μL P17 RVS Primer 1 μM 4 μL Dengue Virus FWD Primer 1 μM 4μL Dengue Virus RVS Primer 1 μM 4 μL Probes Poly Protease Probe 1 800 nM4 μL P17 Probe 1 400 nM 4 μL Dengue Virus Probe 1 200 nM 4 μL

TABLE 21 Binary FAM Experiment 4 Cocktail: HIV polyprotease and HIV p17Concentration Volume Added Reagents UltraPure Water — 54 μL Taq 5xMaster Mix — 25 μL Templates Poly Protease Template 17 nM 4 μL P17Template 15 nM 4 μL Dengue Virus Template 17 nM — Primers Poly ProteaseFWD Primer 1 μM 4 μL Poly Protease RVS Primer 1 μM 4 μL P17 FWD Primer 1μM 4 μL P17 RVS Primer 1 μM 4 μL Dengue Virus FWD Primer 1 μM 4 μLDengue Virus RVS Primer 1 μM 4 μL Probes Poly Protease Probe 1 800 nM 4μL P17 Probe 1 400 nM 4 μL Dengue Virus Probe 1 200 nM 4 μL

TABLE 22 Binary FAM Experiment 5 Cocktail: dengue virus ConcentrationVolume Added Reagents UltraPure Water — 58 μL Taq 5x Master Mix — 25 μLTemplates Poly Protease Template 17 nM — P17 Template 15 nM — DengueVirus Template 17 nM 4 μL Primers Poly Protease FWD Primer 1 μM 4 μLPoly Protease RVS Primer 1 μM 4 μL P17 FWD Primer 1 μM 4 μL P17 RVSPrimer 1 μM 4 μL Dengue Virus FWD Primer 1 μM 4 μL Dengue Virus RVSPrimer 1 μM 4 μL Probes Poly Protease Probe 1 800 nM 4 μL P17 Probe 1400 nM 4 μL Dengue Virus Probe 1 200 nM 4 μL

TABLE 23 Binary FAM Experiment 6 Cocktail: HIV p17 Concentration VolumeAdded Reagents UltraPure Water — 58 μL Taq 5x Master Mix — 25 μLTemplates Poly Protease Template 17 nM — P17 Template 15 nM 4 μL DengueVirus Template 17 nM — Primers Poly Protease FWD Primer 1 μM 4 μL PolyProtease RVS Primer 1 μM 4 μL P17 FWD Primer 1 μM 4 μL P17 RVS Primer 1μM 4 μL Dengue Virus FWD Primer 1 μM 4 μL Dengue Virus RVS Primer 1 1 μM4 μL Probes Poly Protease Probe 1 800 nM 4 μL P17 Probe 1 400 nM 4 μLDengue Virus Probe 1 200 nM 4 μL

TABLE 24 Binary FAM Experiment 7 Cocktail: HIV polyproteaseConcentration Volume Added Reagents UltraPure Water — 58 μL Taq 5xMaster Mix — 25 μL Templates Poly Protease Template 17 nM 4 μL P17Template 15 nM — Dengue Virus Template 17 nM — Primers Poly Protease FWDPrimer 1 μM 4 μL Poly Protease RVS Primer 1 μM 4 μL P17 FWD Primer 1 μM4 μL P17 RVS Primer 1 μM 4 μL Dengue Virus FWD Primer 1 μM 4 μL DengueVirus RVS Primer 1 μM 4 μL Probes Poly Protease Probe 1 800 nM 4 μL P17Probe 1 400 nM 4 μL Dengue Virus Probe 1 200 nM 4 μL

The total fluorescence signal of each experiment was plotted on achromatogram (FIG. 7 ) that was constructed as described above. Thewidth of the bands around each positive control measurement is thepropagated uncertainty of the 1× measurement. That uncertainty wasequated to the standard deviation of the fluorescence signals of thelast five PCR cycles in saturation.

FIG. 7 shows the results of this experiment. The three right-mostresults show the measured intensities for dengue virus alone (DEN), HIVp17 alone (P17), and HIV polyprotease (TPP). The assigned intensitiesfor each of these analytes were as indicated in Table 11, and FIG. 7confirms that the three analytes yielded the expected intensity resultswhen alone (see DEN, P17, and TPP). At the end of the assay, essentiallyall of the probes have been hydrolyzed, releasing essentially all of thefluorophores, which emit a signal. A fixed amount of a fluorophoreproduces a fixed and predictable amount of signal. Therefore a targetthat is present should generally produce a fixed amount of signal, asdetermined by the amount of probe added to the reaction volume.

As expected, the intensity values for the combinations of analytes areequivalent to the sum of the assigned intensities. Since this codingscheme is designed to be non-degenerate, each result can beunambiguously decoded into the presence or absence of a particularanalyte. For example, starting from the left side of FIG. 7 , a resultof 7 indicates the presence of all three analytes. A result of 3indicates the presence of dengue virus and HIV p17 analytes, and theabsence of HIV polyprotease. A result of 5 indicates the presence ofdengue virus and HIV polyprotease, and the absence of HIV p17. Finally aresult of 6 indicates the presence of HIV p17 and HIV polyprotease, andthe absence of dengue virus. This coding scheme can be extended toencode additional analytes, as described elsewhere in this disclosure.

What is claimed is:
 1. A method of unambiguously detecting any uniquecombination of presence or absence of a plurality of analytes, themethod comprising: (a) providing a sample from a subject comprising, orpotentially comprising, said plurality of analytes, (b) forming amixture of said sample and hybridization probes, wherein at least one ofsaid hybridization probes is configured to bind to at least one of saidplurality of analytes corresponding with a respiratory viral pathogen,and wherein said hybridization probes further comprise at least onefluorophore and at most four fluorophores; (c) exciting said at leastone fluorophore to generate one or more signals if one or more of saidplurality of analytes is present, wherein said one or more signalscomprise at least one signal generated by excitement of said one or morefluorophores; (d) measuring said one or more signals to generate acumulative intensity measurement, wherein said cumulative intensitymeasurement corresponds to the presence of a unique combination ofpresence or absence of said plurality of analytes in said sample; and(e) determining whether said at least one of said plurality of analytescorresponding with said respiratory viral pathogen is present, in anyunique combination of presence or absence, based on said cumulativeintensity measurement, wherein the method does not require any step ofimmobilization of said plurality of polynucleotide analytes or massspectrometry, and wherein each analyte is derived from a respiratoryviral pathogen.
 2. The method of claim 1, wherein said respiratory viralpathogen is selected from influenza virus and respiratory syncytialvirus (RSV).
 3. The method of claim 1, wherein said plurality ofanalytes are derived from at least three respiratory viral pathogens. 4.The method of claim 1, wherein said plurality of analytes comprise atleast five analytes.
 5. The method of claim 1, wherein said plurality ofanalytes comprise at least seven analytes.
 6. The method of claim 1,wherein the sample is derived from saliva, blood, or urine from thesubject.
 7. The method of claim 1, wherein the detecting the presence orabsence of at least one of said plurality of analytes indicates thepresence of an infection with said at least one pathogen in saidsubject.
 8. The method of claim 1, further comprising providinginformation concerning the presence or absence of said plurality ofanalytes to a health care professional, wherein the health careprofessional makes a clinical decision based on said information.
 9. Themethod of claim 8, wherein said clinical decision is a treatmentdecision.
 10. The method of claim 9, wherein said treatment decisioncomprises treatment with an anti-viral.
 11. The method of claim 1,further comprising amplifying the analytes.